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Zinc in PDB 5nde: Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222, PDB code: 5nde was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.26 / 1.70
Space group P 42 2 2
Cell size a, b, c (Å), α, β, γ (°) 130.740, 130.740, 100.860, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 17.3

Other elements in 5nde:

The structure of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222 (pdb code 5nde). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222, PDB code: 5nde:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5nde

Go back to Zinc Binding Sites List in 5nde
Zinc binding site 1 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222


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 Metallo-Beta-Lactamase Spm-1 in Space Group P4222 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:20.3
occ:0.94
 OD1 A:ASP37 1.9 27.9 1.0
NE2 A:HIS35 2.1 25.1 1.0
CG A:ASP37 2.9 45.4 1.0
CE1 A:HIS35 3.0 39.9 1.0
O A:HOH501 3.0 39.5 1.0
CD2 A:HIS35 3.1 24.3 1.0
OD2 A:ASP37 3.3 34.6 1.0
O A:HOH654 4.0 41.3 1.0
ND1 A:HIS35 4.2 33.7 1.0
CG A:HIS35 4.2 25.2 1.0
CB A:ASP37 4.3 42.6 1.0
CA A:ASP37 4.9 31.6 1.0
CG2 A:THR43 5.0 27.5 1.0

Zinc binding site 2 out of 6 in 5nde

Go back to Zinc Binding Sites List in 5nde
Zinc binding site 2 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222


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 Metallo-Beta-Lactamase Spm-1 in Space Group P4222 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:21.7
occ:1.00
 ND1 A:HIS110 2.0 21.1 1.0
NE2 A:HIS197 2.1 22.2 1.0
NE2 A:HIS108 2.1 19.5 1.0
CE1 A:HIS110 2.9 21.1 1.0
CD2 A:HIS108 3.0 20.6 1.0
CG A:HIS110 3.0 20.6 1.0
CD2 A:HIS197 3.1 20.4 1.0
CE1 A:HIS197 3.1 24.7 1.0
CE1 A:HIS108 3.2 20.6 1.0
ZN A:ZN403 3.4 23.7 0.8
CB A:HIS110 3.4 20.1 1.0
O1 A:GOL411 3.6 40.5 1.0
OD1 A:ASP112 4.0 23.2 1.0
O A:HOH511 4.0 35.3 1.0
NE2 A:HIS110 4.1 24.2 1.0
SG A:CYS222 4.1 23.4 1.0
CD2 A:HIS110 4.1 23.6 1.0
CB A:CYS222 4.1 23.2 1.0
CG A:HIS108 4.2 19.8 1.0
ND1 A:HIS197 4.2 21.6 1.0
CG A:HIS197 4.2 18.6 1.0
ND1 A:HIS108 4.2 22.6 1.0
OD2 A:ASP112 4.4 30.8 1.0
C1 A:GOL411 4.5 28.8 1.0
C3 A:GOL410 4.6 80.6 1.0
CG A:ASP112 4.6 26.1 1.0
O2 A:GOL411 4.6 67.0 1.0
O2 A:GOL410 4.7 75.9 1.0
O3 A:GOL410 4.9 83.5 1.0
CA A:HIS110 4.9 18.8 1.0

Zinc binding site 3 out of 6 in 5nde

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Zinc binding site 3 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222


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 Metallo-Beta-Lactamase Spm-1 in Space Group P4222 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:23.7
occ:0.82
 O1 A:GOL411 2.0 40.5 1.0
NE2 A:HIS264 2.0 25.8 1.0
OD2 A:ASP112 2.1 30.8 1.0
SG A:CYS222 2.2 23.4 1.0
CD2 A:HIS264 3.0 27.1 1.0
CE1 A:HIS264 3.0 26.8 1.0
CG A:ASP112 3.1 26.1 1.0
OD1 A:ASP112 3.3 23.2 1.0
C1 A:GOL411 3.4 28.8 1.0
CB A:CYS222 3.4 23.2 1.0
ZN A:ZN402 3.4 21.7 1.0
O A:HOH511 3.5 35.3 1.0
ND1 A:HIS264 4.1 23.0 1.0
CG A:HIS264 4.1 24.9 1.0
C2 A:GOL411 4.1 49.1 1.0
CE1 A:HIS108 4.2 20.6 1.0
NE2 A:HIS108 4.2 19.5 1.0
NE2 A:HIS197 4.3 22.2 1.0
O2 A:GOL411 4.4 67.0 1.0
CB A:ASP112 4.4 18.6 1.0
CA A:CYS222 4.6 20.0 1.0
CE1 A:HIS197 4.7 24.7 1.0
O A:HOH577 4.8 24.0 1.0
O A:GLY263 4.9 22.6 1.0
O A:ASP112 4.9 22.2 1.0
CA A:GLY263 4.9 20.2 1.0
C A:GLY263 4.9 21.0 1.0
O A:HOH629 5.0 25.1 1.0

Zinc binding site 4 out of 6 in 5nde

Go back to Zinc Binding Sites List in 5nde
Zinc binding site 4 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222


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 Metallo-Beta-Lactamase Spm-1 in Space Group P4222 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:25.1
occ:1.00
 ND1 A:HIS165 2.0 26.0 1.0
OE2 A:GLU118 2.1 24.7 1.0
CD A:GLU118 2.9 31.7 1.0
CE1 A:HIS165 2.9 26.7 1.0
CG A:HIS165 3.0 28.1 1.0
OE1 A:GLU118 3.1 31.6 1.0
CB A:HIS165 3.4 27.2 1.0
O A:HOH556 3.8 29.6 1.0
NE2 A:HIS165 4.0 29.1 1.0
O A:HIS165 4.0 31.1 1.0
CD2 A:HIS165 4.1 27.9 1.0
N A:HIS165 4.1 28.2 1.0
CG A:GLU118 4.2 27.5 1.0
CA A:HIS165 4.3 25.4 1.0
C A:HIS165 4.6 27.1 1.0
ND2 A:ASN83 4.9 27.0 1.0

Zinc binding site 5 out of 6 in 5nde

Go back to Zinc Binding Sites List in 5nde
Zinc binding site 5 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222


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 Metallo-Beta-Lactamase Spm-1 in Space Group P4222 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:22.0
occ:1.00
 ND1 B:HIS110 2.1 20.8 1.0
NE2 B:HIS197 2.1 21.8 1.0
NE2 B:HIS108 2.1 18.5 1.0
O B:HOH638 2.2 27.1 1.0
CD2 B:HIS108 3.0 18.2 1.0
CD2 B:HIS197 3.0 20.3 1.0
CE1 B:HIS110 3.0 23.3 1.0
CG B:HIS110 3.1 19.7 1.0
CE1 B:HIS197 3.1 24.3 1.0
CE1 B:HIS108 3.2 19.9 1.0
CB B:HIS110 3.4 16.9 1.0
ZN B:ZN402 3.5 27.3 0.9
O B:HOH507 3.8 38.9 1.0
OD1 B:ASP112 3.9 22.4 1.0
SG B:CYS222 4.1 26.7 1.0
NE2 B:HIS110 4.1 24.1 1.0
CB B:CYS222 4.2 23.1 1.0
CD2 B:HIS110 4.2 21.4 1.0
CG B:HIS197 4.2 19.4 1.0
ND1 B:HIS197 4.2 20.6 1.0
CG B:HIS108 4.2 17.2 1.0
O1 B:GOL404 4.2 30.9 1.0
ND1 B:HIS108 4.2 19.9 1.0
OD2 B:ASP112 4.4 25.9 1.0
CG B:ASP112 4.6 23.9 1.0
C1 B:GOL404 4.9 42.7 1.0
CA B:HIS110 4.9 17.2 1.0

Zinc binding site 6 out of 6 in 5nde

Go back to Zinc Binding Sites List in 5nde
Zinc binding site 6 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222


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 Metallo-Beta-Lactamase Spm-1 in Space Group P4222 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:27.3
occ:0.86
 O B:HOH638 1.9 27.1 1.0
OD2 B:ASP112 2.1 25.9 1.0
NE2 B:HIS264 2.1 23.1 1.0
SG B:CYS222 2.2 26.7 1.0
O1 B:GOL404 2.9 30.9 1.0
CD2 B:HIS264 3.0 28.7 1.0
CE1 B:HIS264 3.1 26.8 1.0
CG B:ASP112 3.1 23.9 1.0
O B:HOH507 3.3 38.9 1.0
CB B:CYS222 3.4 23.1 1.0
OD1 B:ASP112 3.4 22.4 1.0
ZN B:ZN401 3.5 22.0 1.0
O B:HOH501 3.5 40.1 1.0
O B:HOH561 4.1 59.2 1.0
C1 B:GOL404 4.2 42.7 1.0
ND1 B:HIS264 4.2 24.5 1.0
CG B:HIS264 4.2 25.1 1.0
O2 B:GOL404 4.2 70.5 1.0
CE1 B:HIS108 4.2 19.9 1.0
NE2 B:HIS108 4.2 18.5 1.0
NE2 B:HIS197 4.3 21.8 1.0
CB B:ASP112 4.4 16.9 1.0
CA B:CYS222 4.6 25.6 1.0
CE1 B:HIS197 4.7 24.3 1.0
C2 B:GOL404 4.8 66.1 1.0
O B:GLY263 4.9 23.0 1.0
CA B:GLY263 5.0 20.3 1.0
O B:ASP112 5.0 19.4 1.0
O B:HOH652 5.0 28.9 1.0
C B:GLY263 5.0 25.1 1.0

Reference:

M.I.Abboud, M.Kosmopoulou, A.P.Krismanich, J.W.Johnson, P.Hinchliffe, J.Brem, T.D.W.Claridge, J.Spencer, C.J.Schofield, G.I.Dmitrienko. Cyclobutanone Mimics of Intermediates in Metallo-Beta-Lactamase Catalysis. Chemistry V. 24 5734 2018.
ISSN: ISSN 1521-3765
PubMed: 29250863
DOI: 10.1002/CHEM.201705886
Page generated: Sun Oct 27 22:45:30 2024

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