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Zinc in PDB 1m2x: Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril

Enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril

All present enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril, PDB code: 1m2x was solved by I.Garcia-Saez, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.50
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 159.685, 159.685, 97.815, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 20.8

Other elements in 1m2x:

The structure of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril (pdb code 1m2x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril, PDB code: 1m2x:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 1m2x

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Zinc binding site 1 out of 12 in the Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:8.7
occ:1.00
 ND1 A:HIS118 2.0 7.6 1.0
NE2 A:HIS196 2.1 7.1 1.0
NE2 A:HIS116 2.2 9.9 1.0
S A:MCO811 2.3 11.0 1.0
CE1 A:HIS118 3.0 7.2 1.0
CG A:HIS118 3.0 7.1 1.0
CD2 A:HIS196 3.0 6.8 1.0
CE1 A:HIS196 3.1 7.9 1.0
CE1 A:HIS116 3.1 8.8 1.0
CD2 A:HIS116 3.2 9.1 1.0
C1 A:MCO811 3.2 13.8 1.0
CB A:HIS118 3.4 8.0 1.0
ZN A:ZN902 3.7 9.1 0.8
C2 A:MCO811 3.9 14.1 1.0
NE2 A:HIS118 4.1 8.8 1.0
CD2 A:HIS118 4.1 8.3 1.0
ND1 A:HIS196 4.2 6.9 1.0
CG A:HIS196 4.2 7.3 1.0
ND1 A:HIS116 4.2 8.8 1.0
OD1 A:ASP120 4.2 9.7 1.0
CG A:HIS116 4.3 7.1 1.0
CB A:CYS221 4.3 9.6 1.0
SG A:CYS221 4.4 10.8 1.0
CG2 A:THR197 4.5 7.6 1.0
CA A:HIS118 4.8 7.7 1.0
C3 A:MCO811 4.9 14.2 1.0
OD2 A:ASP120 4.9 11.0 1.0
C4 A:MCO811 5.0 16.6 1.0

Zinc binding site 2 out of 12 in 1m2x

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Zinc binding site 2 out of 12 in the Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:9.1
occ:0.80
 NE2 A:HIS263 2.1 8.7 1.0
OD2 A:ASP120 2.1 11.0 1.0
S A:MCO811 2.3 11.0 1.0
SG A:CYS221 2.3 10.8 1.0
CD2 A:HIS263 3.0 10.5 1.0
CE1 A:HIS263 3.1 9.2 1.0
CG A:ASP120 3.1 9.9 1.0
OD1 A:ASP120 3.4 9.7 1.0
C1 A:MCO811 3.4 13.8 1.0
CB A:CYS221 3.5 9.6 1.0
ZN A:ZN901 3.7 8.7 1.0
NH2 A:ARG121 4.0 12.3 1.0
NE A:ARG121 4.1 9.4 1.0
ND1 A:HIS263 4.1 9.6 1.0
CG A:HIS263 4.2 10.6 1.0
CE1 A:HIS116 4.3 8.8 1.0
CB A:ASP120 4.4 8.8 1.0
NE2 A:HIS116 4.5 9.9 1.0
NE2 A:HIS196 4.5 7.1 1.0
CZ A:ARG121 4.5 9.4 1.0
O A:HOH1040 4.6 19.0 1.0
O A:HOH948 4.7 17.3 1.0
CA A:CYS221 4.7 10.1 1.0
C2 A:MCO811 4.7 14.1 1.0
CE1 A:HIS196 4.8 7.9 1.0

Zinc binding site 3 out of 12 in 1m2x

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Zinc binding site 3 out of 12 in the Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn900

b:21.5
occ:0.70
 OD1 A:ASP288 2.2 20.2 1.0
O A:HOH1085 2.5 24.8 1.0
O A:HOH1084 2.7 32.5 1.0
O A:HOH1086 2.7 38.0 1.0
ND1 A:HIS285 2.9 22.0 1.0
CG A:ASP288 3.2 18.7 1.0
CA A:HIS285 3.4 17.7 1.0
CB A:ASP288 3.5 16.9 1.0
CB A:HIS285 3.6 18.7 1.0
CG A:HIS285 3.7 21.6 1.0
CE1 A:HIS285 4.0 23.4 1.0
N A:HIS285 4.1 17.4 1.0
OD2 A:ASP288 4.3 20.4 1.0
C A:HIS285 4.4 16.3 1.0
O A:HIS285 4.4 17.0 1.0
O A:GLN284 4.5 20.0 1.0
C A:GLN284 4.6 18.1 1.0
CG A:GLN284 4.9 18.1 0.3
CD2 A:HIS285 4.9 22.3 1.0
CA A:ASP288 4.9 14.9 1.0

Zinc binding site 4 out of 12 in 1m2x

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Zinc binding site 4 out of 12 in the Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:8.6
occ:1.00
 ND1 B:HIS118 2.1 7.1 1.0
NE2 B:HIS196 2.1 7.2 1.0
NE2 B:HIS116 2.1 8.7 1.0
S B:MCO812 2.3 11.1 1.0
CE1 B:HIS116 3.0 7.9 1.0
CG B:HIS118 3.0 6.8 1.0
CD2 B:HIS196 3.0 6.3 1.0
CE1 B:HIS118 3.0 7.2 1.0
CE1 B:HIS196 3.1 7.6 1.0
CD2 B:HIS116 3.1 8.6 1.0
C1 B:MCO812 3.2 13.2 1.0
CB B:HIS118 3.3 6.9 1.0
ZN B:ZN902 3.7 9.0 0.8
C2 B:MCO812 3.9 13.8 1.0
NE2 B:HIS118 4.1 8.0 1.0
ND1 B:HIS116 4.2 8.8 1.0
CD2 B:HIS118 4.2 8.2 1.0
OD1 B:ASP120 4.2 10.3 1.0
ND1 B:HIS196 4.2 7.1 1.0
CG B:HIS196 4.2 6.0 1.0
CG B:HIS116 4.2 7.6 1.0
CB B:CYS221 4.3 10.9 1.0
SG B:CYS221 4.3 10.9 1.0
CG2 B:THR197 4.6 7.3 1.0
CA B:HIS118 4.8 7.5 1.0
OD2 B:ASP120 4.9 10.3 1.0
C3 B:MCO812 4.9 13.2 1.0
CG B:ASP120 5.0 10.2 1.0
C4 B:MCO812 5.0 16.0 1.0

Zinc binding site 5 out of 12 in 1m2x

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Zinc binding site 5 out of 12 in the Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:9.0
occ:0.80
 OD2 B:ASP120 2.1 10.3 1.0
NE2 B:HIS263 2.1 10.0 1.0
S B:MCO812 2.3 11.1 1.0
SG B:CYS221 2.3 10.9 1.0
CG B:ASP120 3.1 10.2 1.0
CD2 B:HIS263 3.1 10.0 1.0
CE1 B:HIS263 3.1 10.0 1.0
OD1 B:ASP120 3.4 10.3 1.0
C1 B:MCO812 3.4 13.2 1.0
CB B:CYS221 3.5 10.9 1.0
ZN B:ZN901 3.7 8.6 1.0
NH2 B:ARG121 3.9 11.8 1.0
NE B:ARG121 4.1 9.4 1.0
ND1 B:HIS263 4.2 11.2 1.0
CG B:HIS263 4.2 9.9 1.0
CE1 B:HIS116 4.3 7.9 1.0
CB B:ASP120 4.4 9.1 1.0
CZ B:ARG121 4.5 9.9 1.0
NE2 B:HIS116 4.5 8.7 1.0
O B:HOH1035 4.5 21.2 1.0
NE2 B:HIS196 4.5 7.2 1.0
O B:HOH981 4.7 18.3 1.0
CA B:CYS221 4.8 10.0 1.0
C2 B:MCO812 4.8 13.8 1.0
CE1 B:HIS196 4.9 7.6 1.0

Zinc binding site 6 out of 12 in 1m2x

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Zinc binding site 6 out of 12 in the Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn900

b:21.3
occ:0.70
 OD1 B:ASP288 2.3 21.6 1.0
ND1 B:HIS285 2.4 25.4 1.0
O A:HOH1087 2.6 31.2 1.0
O B:HOH1071 2.7 33.2 1.0
O B:HOH1070 2.7 36.5 1.0
CG B:ASP288 3.2 19.1 1.0
CG B:HIS285 3.4 23.1 1.0
CE1 B:HIS285 3.4 24.7 1.0
CB B:ASP288 3.5 17.3 1.0
CA B:HIS285 3.6 17.5 1.0
CB B:HIS285 3.6 20.9 1.0
OE1 A:GLN284 4.3 19.4 0.3
O B:HIS285 4.3 17.6 1.0
OD2 B:ASP288 4.4 19.8 1.0
C B:HIS285 4.5 17.5 1.0
NE2 B:HIS285 4.5 26.7 1.0
CD2 B:HIS285 4.5 24.8 1.0
N B:HIS285 4.6 18.0 1.0
O B:GLN284 4.8 19.7 1.0
CA B:ASP288 5.0 15.6 1.0

Zinc binding site 7 out of 12 in 1m2x

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Zinc binding site 7 out of 12 in the Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn901

b:8.3
occ:1.00
 NE2 C:HIS196 2.0 6.4 1.0
NE2 C:HIS116 2.1 9.4 1.0
ND1 C:HIS118 2.1 8.4 1.0
S C:MCO813 2.3 11.4 1.0
CD2 C:HIS196 3.0 6.0 1.0
CE1 C:HIS116 3.0 8.4 1.0
CG C:HIS118 3.1 6.6 1.0
CE1 C:HIS196 3.1 7.8 1.0
CE1 C:HIS118 3.1 7.1 1.0
CD2 C:HIS116 3.1 7.9 1.0
C1 C:MCO813 3.3 14.7 1.0
CB C:HIS118 3.4 6.2 1.0
ZN C:ZN902 3.7 8.9 0.8
C2 C:MCO813 4.0 13.9 1.0
ND1 C:HIS116 4.1 8.6 1.0
CG C:HIS196 4.1 5.6 1.0
ND1 C:HIS196 4.2 7.5 1.0
NE2 C:HIS118 4.2 7.7 1.0
CD2 C:HIS118 4.2 7.8 1.0
CG C:HIS116 4.2 7.6 1.0
OD1 C:ASP120 4.2 9.6 1.0
CB C:CYS221 4.3 10.7 1.0
SG C:CYS221 4.3 11.0 1.0
CG2 C:THR197 4.6 6.5 1.0
CA C:HIS118 4.8 7.9 1.0
OD2 C:ASP120 5.0 10.3 1.0
C3 C:MCO813 5.0 13.9 1.0

Zinc binding site 8 out of 12 in 1m2x

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Zinc binding site 8 out of 12 in the Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn902

b:8.9
occ:0.80
 NE2 C:HIS263 2.1 9.0 1.0
OD2 C:ASP120 2.2 10.3 1.0
SG C:CYS221 2.3 11.0 1.0
S C:MCO813 2.3 11.4 1.0
CD2 C:HIS263 3.1 8.7 1.0
CG C:ASP120 3.1 10.2 1.0
CE1 C:HIS263 3.1 9.0 1.0
OD1 C:ASP120 3.3 9.6 1.0
C1 C:MCO813 3.4 14.7 1.0
CB C:CYS221 3.5 10.7 1.0
ZN C:ZN901 3.7 8.3 1.0
NH2 C:ARG121 3.9 11.2 1.0
NE C:ARG121 4.1 8.9 1.0
ND1 C:HIS263 4.2 9.6 1.0
CG C:HIS263 4.2 10.2 1.0
CE1 C:HIS116 4.3 8.4 1.0
CB C:ASP120 4.4 9.2 1.0
NE2 C:HIS116 4.4 9.4 1.0
CZ C:ARG121 4.5 9.1 1.0
NE2 C:HIS196 4.5 6.4 1.0
O C:HOH999 4.6 18.4 1.0
O C:HOH954 4.6 15.7 1.0
CA C:CYS221 4.7 9.9 1.0
C2 C:MCO813 4.8 13.9 1.0
CE1 C:HIS196 4.8 7.8 1.0

Zinc binding site 9 out of 12 in 1m2x

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Zinc binding site 9 out of 12 in the Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn900

b:20.6
occ:0.70
 OD1 C:ASP288 2.2 20.7 1.0
ND1 C:HIS285 2.4 21.6 1.0
O D:HOH1089 2.7 34.6 1.0
O C:HOH1074 2.9 40.0 1.0
O C:HOH1075 2.9 48.2 1.0
CG C:ASP288 3.2 17.9 1.0
CE1 C:HIS285 3.4 20.4 1.0
CG C:HIS285 3.4 19.9 1.0
CB C:ASP288 3.4 15.5 0.5
CA C:HIS285 3.5 16.4 1.0
CB C:HIS285 3.6 18.8 1.0
O C:HIS285 4.3 15.4 1.0
OD2 C:ASP288 4.3 19.5 1.0
OE1 D:GLN284 4.4 25.6 0.5
C C:HIS285 4.5 15.3 1.0
NE2 C:HIS285 4.5 22.8 1.0
N C:HIS285 4.5 17.0 1.0
CD2 C:HIS285 4.6 21.7 1.0
O C:GLN284 4.7 18.8 1.0
CA C:ASP288 4.9 15.2 1.0
C C:GLN284 5.0 17.0 1.0

Zinc binding site 10 out of 12 in 1m2x

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Zinc binding site 10 out of 12 in the Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Metallo-Beta-Lactamase Blab of Chryseobacterium Meningosepticum in Complex with the Inhibitor D- Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn901

b:8.5
occ:1.00
 ND1 D:HIS118 2.0 8.2 1.0
NE2 D:HIS116 2.1 8.9 1.0
NE2 D:HIS196 2.1 7.9 1.0
S D:MCO814 2.4 10.7 1.0
CE1 D:HIS118 3.0 7.7 1.0
CG D:HIS118 3.0 7.6 1.0
CE1 D:HIS116 3.0 10.2 1.0
CD2 D:HIS196 3.1 6.3 1.0
CE1 D:HIS196 3.1 6.7 1.0
CD2 D:HIS116 3.1 8.7 1.0
C1 D:MCO814 3.2 12.4 1.0
CB D:HIS118 3.3 8.2 1.0
ZN D:ZN902 3.7 9.3 0.8
C2 D:MCO814 3.9 13.6 1.0
NE2 D:HIS118 4.1 8.3 1.0
CD2 D:HIS118 4.1 8.3 1.0
ND1 D:HIS116 4.1 9.2 1.0
OD1 D:ASP120 4.2 10.6 1.0
ND1 D:HIS196 4.2 6.8 1.0
CG D:HIS116 4.2 7.5 1.0
CG D:HIS196 4.2 5.8 1.0
CB D:CYS221 4.3 9.4 1.0
SG D:CYS221 4.4 10.6 1.0
CG2 D:THR197 4.5 7.5 1.0
CA D:HIS118 4.7 8.3 1.0
C3 D:MCO814 4.9 13.3 1.0
OD2 D:ASP120 4.9 10.2 1.0
N D:HIS118 5.0 7.8 1.0
C4 D:MCO814 5.0 15.8 1.0
CG D:ASP120 5.0 9.6 1.0

Reference:

I.Garcia-Saez, J.Hopkins, C.Papamicael, N.Franceschini, G.Amicosante, G.M.Rossolini, M.Galleni, J.M.Frere, O.Dideberg. The 1.5 A Structure of Chryseobacterium Meningosepticum Zn-Beta-Lactamase in Complex with the Inhibitor, D-Captopril J.Biol.Chem. V. 278 23868 2003.
ISSN: ISSN 0021-9258
PubMed: 12684522
DOI: 10.1074/JBC.M301062200
Page generated: Sun Oct 13 05:18:41 2024

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