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Zinc in PDB 5k1s: Crystal Structure of Aibc

Protein crystallography data

The structure of Crystal Structure of Aibc, PDB code: 5k1s was solved by T.Bock, R.Mueller, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.94 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.294, 77.427, 309.638, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 26.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Aibc (pdb code 5k1s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Aibc, PDB code: 5k1s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5k1s

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Zinc binding site 1 out of 8 in the Crystal Structure of Aibc


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 Aibc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:67.5
occ:1.00
SG A:CYS98 2.2 51.4 1.0
SG A:CYS95 2.3 61.2 1.0
SG A:CYS92 2.3 62.7 1.0
SG A:CYS106 2.4 45.8 1.0
HB2 A:CYS106 2.9 70.2 1.0
H A:GLY93 2.9 73.3 1.0
HB2 A:CYS98 3.0 84.6 1.0
H A:CYS95 3.1 85.7 1.0
CB A:CYS106 3.2 47.3 1.0
H A:CYS92 3.2 69.1 1.0
CB A:CYS98 3.3 53.1 1.0
H A:CYS98 3.5 76.1 1.0
HB3 A:CYS95 3.5 75.2 1.0
CB A:CYS95 3.5 60.2 1.0
HG1 A:THR108 3.5 91.3 1.0
OG1 A:THR108 3.7 64.6 1.0
CB A:CYS92 3.7 61.2 1.0
N A:GLY93 3.7 52.2 1.0
H A:ASP94 3.7 95.0 1.0
HA A:CYS106 3.7 70.4 1.0
HB3 A:CYS92 3.8 77.5 1.0
N A:CYS95 3.8 63.9 1.0
N A:CYS92 3.8 62.0 1.0
HG A:SER91 3.9 93.3 1.0
HB3 A:CYS98 4.0 84.6 1.0
HB3 A:CYS106 4.0 70.2 1.0
CA A:CYS106 4.1 46.2 1.0
N A:CYS98 4.1 53.8 1.0
CA A:CYS92 4.1 62.3 1.0
CA A:CYS95 4.2 62.9 1.0
H A:THR108 4.2 73.8 1.0
CA A:CYS98 4.3 53.9 1.0
OG A:SER91 4.3 59.9 1.0
N A:ASP94 4.3 79.5 1.0
HB2 A:CYS95 4.3 75.2 1.0
C A:CYS92 4.4 64.1 1.0
HB2 A:CYS92 4.4 77.5 1.0
HB2 A:LEU97 4.4 67.0 1.0
HA A:CYS98 4.6 78.7 1.0
CA A:GLY93 4.6 53.5 1.0
HA2 A:GLY93 4.6 77.2 1.0
H A:LYS107 4.6 63.1 1.0
HG23 A:THR108 4.7 71.7 1.0
O A:CYS95 4.7 66.5 1.0
C A:CYS95 4.8 65.0 1.0
H A:ASP109 4.8 67.9 1.0
HA A:SER91 4.8 70.1 1.0
C A:GLY93 4.8 54.6 1.0
C A:SER91 4.8 58.0 1.0
CB A:THR108 4.9 61.5 1.0
C A:ASP94 4.9 79.9 1.0
C A:CYS106 4.9 43.1 1.0

Zinc binding site 2 out of 8 in 5k1s

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Zinc binding site 2 out of 8 in the Crystal Structure of Aibc


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 Aibc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:70.3
occ:1.00
NE2 A:HIS62 2.0 50.1 1.0
SG A:CYS149 2.3 53.4 1.0
SG A:CYS40 2.5 57.1 1.0
HE1 A:HIS62 2.5 58.0 1.0
CE1 A:HIS62 2.6 49.3 1.0
HB2 A:CYS40 3.1 56.5 1.0
HB3 A:CYS149 3.1 53.4 1.0
CB A:CYS40 3.2 56.5 1.0
HB3 A:CYS40 3.3 56.5 1.0
CD2 A:HIS62 3.3 49.8 1.0
CB A:CYS149 3.3 55.7 1.0
HG2 A:GLN88 3.6 56.1 1.0
HD2 A:HIS62 3.7 63.2 1.0
HB3 A:HIS42 3.7 53.7 1.0
HB2 A:CYS149 3.8 53.4 1.0
ND1 A:HIS62 3.8 48.6 1.0
HE21 A:GLN88 3.8 56.9 1.0
HB2 A:HIS42 3.9 53.7 1.0
CG A:HIS62 4.2 48.9 1.0
CB A:HIS42 4.3 40.5 1.0
CG A:GLN88 4.5 43.8 1.0
HA A:CYS149 4.5 76.0 1.0
HD1 A:HIS62 4.5 69.2 1.0
NE2 A:GLN88 4.5 46.6 1.0
CA A:CYS149 4.6 57.8 1.0
HG3 A:GLN88 4.6 56.1 1.0
OE1 A:GLU63 4.6 58.8 1.0
H A:HIS42 4.7 64.7 1.0
CA A:CYS40 4.7 57.5 1.0
HB2 A:GLU63 4.8 72.7 1.0
CG A:HIS42 4.9 40.4 1.0
HA A:CYS40 5.0 80.7 1.0
CD A:GLU63 5.0 60.0 1.0
CD A:GLN88 5.0 45.8 1.0

Zinc binding site 3 out of 8 in 5k1s

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Zinc binding site 3 out of 8 in the Crystal Structure of Aibc


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 Aibc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:61.3
occ:1.00
SG C:CYS95 2.3 47.1 1.0
SG C:CYS98 2.3 43.4 1.0
SG C:CYS106 2.3 43.9 1.0
SG C:CYS92 2.4 49.2 1.0
HB2 C:CYS106 3.0 57.9 1.0
H C:CYS92 3.0 59.2 1.0
H C:CYS95 3.1 70.1 1.0
HB3 C:CYS95 3.2 59.3 1.0
H C:GLY93 3.2 52.6 1.0
HB2 C:CYS98 3.2 67.5 1.0
CB C:CYS106 3.2 43.5 1.0
HG1 C:THR108 3.3 83.8 1.0
CB C:CYS95 3.3 47.6 1.0
CB C:CYS98 3.4 43.9 1.0
OG1 C:THR108 3.4 57.1 1.0
CB C:CYS92 3.6 48.1 1.0
H C:CYS98 3.6 62.9 1.0
HB3 C:CYS92 3.7 72.3 1.0
N C:CYS92 3.7 46.2 1.0
HA C:CYS106 3.7 54.3 1.0
N C:GLY93 3.8 51.1 1.0
H C:ASP94 3.9 68.0 1.0
N C:CYS95 3.9 47.0 1.0
HB3 C:CYS106 4.0 57.9 1.0
CA C:CYS92 4.0 46.9 1.0
CA C:CYS106 4.1 44.3 1.0
HB2 C:CYS95 4.1 59.3 1.0
HB3 C:CYS98 4.1 67.5 1.0
HB2 C:SER91 4.1 57.5 1.0
H C:THR108 4.1 61.7 1.0
CA C:CYS95 4.2 47.6 1.0
N C:CYS98 4.2 45.1 1.0
C C:CYS92 4.3 47.0 1.0
HB2 C:LEU97 4.4 67.3 1.0
CA C:CYS98 4.4 44.3 1.0
HB2 C:CYS92 4.4 72.3 1.0
N C:ASP94 4.5 77.1 1.0
H C:LYS107 4.5 49.3 1.0
H C:ASP109 4.6 64.5 1.0
HG23 C:THR108 4.6 70.1 1.0
HA C:CYS98 4.7 71.9 1.0
CB C:THR108 4.7 56.4 1.0
C C:SER91 4.7 52.9 1.0
CA C:GLY93 4.7 51.2 1.0
HA C:SER91 4.8 57.6 1.0
HA2 C:GLY93 4.8 56.9 1.0
C C:CYS95 4.9 47.5 1.0
C C:CYS106 4.9 43.8 1.0
N C:THR108 4.9 55.9 1.0
HG21 C:THR108 4.9 70.1 1.0
N C:LYS107 5.0 48.6 1.0
CB C:SER91 5.0 52.7 1.0
HA C:CYS92 5.0 58.5 1.0
C C:GLY93 5.0 52.1 1.0
HA C:CYS95 5.0 53.1 1.0
O C:CYS95 5.0 47.0 1.0
HA C:ASN103 5.0 59.7 1.0

Zinc binding site 4 out of 8 in 5k1s

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Zinc binding site 4 out of 8 in the Crystal Structure of Aibc


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 Aibc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:89.3
occ:1.00
NE2 C:HIS-9 2.3 47.9 1.0
CD2 C:HIS-9 3.1 47.5 1.0
HD2 C:HIS-9 3.2 44.7 1.0
CE1 C:HIS-9 3.3 47.9 1.0
HE1 C:HIS-9 3.6 54.4 1.0
CG C:HIS-9 4.3 47.2 1.0
ND1 C:HIS-9 4.4 47.5 1.0
HA C:HIS-10 4.8 68.7 1.0

Zinc binding site 5 out of 8 in 5k1s

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Zinc binding site 5 out of 8 in the Crystal Structure of Aibc


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 Aibc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:0.6
occ:1.00
SG B:CYS40 2.2 85.2 1.0
SG B:CYS149 2.4 76.8 1.0
HG B:CYS40 3.1 86.0 1.0
HB2 B:CYS149 3.4 0.4 1.0
CB B:CYS149 3.4 74.7 1.0
HB3 B:CYS40 3.5 0.5 1.0
CB B:CYS40 3.6 84.4 1.0
HB3 B:CYS149 3.6 0.4 1.0
CB B:GLU63 3.6 75.5 1.0
H B:CYS40 4.0 0.6 1.0
H B:GLU63 4.1 82.2 1.0
HB2 B:CYS40 4.1 0.5 1.0
HB3 B:HIS42 4.4 0.4 1.0
HH22 B:ARG337 4.5 88.7 1.0
N B:GLU63 4.6 78.0 1.0
N B:CYS40 4.7 88.8 1.0
CA B:CYS40 4.7 86.6 1.0
CA B:GLU63 4.7 77.1 1.0
CA B:CYS149 4.8 72.6 1.0
OD2 B:ASP43 5.0 89.7 1.0

Zinc binding site 6 out of 8 in 5k1s

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Zinc binding site 6 out of 8 in the Crystal Structure of Aibc


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 Aibc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:0.5
occ:1.00
HB2 B:CYS106 2.1 0.9 1.0
SG B:CYS92 2.4 0.1 1.0
SG B:CYS95 2.4 0.5 1.0
SG B:CYS98 2.5 0.1 1.0
SG B:CYS106 2.5 0.5 1.0
HB3 B:CYS95 2.7 0.5 1.0
CB B:CYS106 2.7 0.6 1.0
CB B:CYS95 3.1 0.7 1.0
HB3 B:CYS106 3.3 0.9 1.0
HG1 B:THR108 3.4 0.9 1.0
HB2 B:CYS98 3.5 0.2 1.0
H B:CYS95 3.6 0.5 1.0
OG1 B:THR108 3.6 0.7 1.0
CB B:CYS98 3.7 0.1 1.0
HB2 B:CYS95 3.7 0.5 1.0
CB B:CYS92 3.7 0.4 1.0
HA B:CYS106 3.8 0.4 1.0
H B:CYS92 3.8 0.3 1.0
HB3 B:CYS92 3.8 0.0 1.0
H B:CYS98 3.8 0.1 1.0
CA B:CYS106 3.9 0.8 1.0
O B:CYS92 3.9 0.3 1.0
N B:CYS95 4.1 0.9 1.0
C B:CYS92 4.2 1.0 1.0
CA B:CYS95 4.2 0.9 1.0
N B:CYS92 4.2 0.2 1.0
CA B:CYS92 4.3 0.8 1.0
H B:THR108 4.4 0.9 1.0
N B:CYS98 4.4 0.7 1.0
HB3 B:CYS98 4.4 0.2 1.0
HB2 B:CYS92 4.5 0.0 1.0
HG23 B:THR108 4.6 1.0 1.0
CA B:CYS98 4.6 0.3 1.0
OG B:SER91 4.7 0.8 1.0
H B:ASP109 4.7 0.7 1.0
HB2 B:LEU97 4.7 0.6 1.0
C B:CYS106 4.8 0.6 1.0
HA B:ASN103 4.8 0.5 1.0
HG21 B:THR108 4.8 1.0 1.0
H B:LYS107 4.8 0.7 1.0
H B:CYS106 4.8 0.3 1.0
HA B:CYS98 4.9 0.5 1.0
CB B:THR108 4.9 0.9 1.0
N B:CYS106 4.9 0.7 1.0
H B:LEU97 4.9 0.3 1.0
HA B:CYS95 4.9 0.5 1.0
CG2 B:THR108 5.0 0.9 1.0

Zinc binding site 7 out of 8 in 5k1s

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Zinc binding site 7 out of 8 in the Crystal Structure of Aibc


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 Aibc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:0.4
occ:1.00
HE2 D:HIS62 1.6 93.2 1.0
NE2 D:HIS62 2.1 92.9 1.0
OE2 D:GLU63 2.2 69.3 1.0
SG D:CYS40 2.3 85.9 1.0
SG D:CYS149 2.3 77.8 1.0
CE1 D:HIS62 2.6 91.5 1.0
HE1 D:HIS62 2.6 1.0 1.0
HG3 D:GLU63 2.8 0.0 1.0
CD D:GLU63 3.1 69.9 1.0
CD2 D:HIS62 3.2 95.0 1.0
CG D:GLU63 3.3 70.7 1.0
HG2 D:GLU63 3.4 0.0 1.0
CB D:CYS149 3.4 75.9 1.0
HB3 D:CYS40 3.5 0.0 1.0
HB3 D:CYS149 3.5 0.9 1.0
HB2 D:CYS149 3.6 0.9 1.0
CB D:CYS40 3.6 85.5 1.0
HD2 D:HIS62 3.7 0.9 1.0
HB3 D:HIS42 3.7 0.6 1.0
ND1 D:HIS62 3.8 92.7 1.0
CG D:HIS62 4.1 94.9 1.0
HB2 D:CYS40 4.1 0.0 1.0
OE1 D:GLU63 4.3 70.0 1.0
HG2 D:GLN88 4.3 0.1 1.0
H D:CYS40 4.4 0.8 1.0
HB2 D:HIS42 4.5 0.6 1.0
CB D:HIS42 4.5 78.3 1.0
HE21 D:GLN88 4.6 93.4 1.0
H D:HIS42 4.7 95.6 1.0
O D:HOH501 4.7 82.8 1.0
HG3 D:GLN88 4.7 0.1 1.0
CA D:CYS40 4.7 88.2 1.0
HD2 D:HIS42 4.7 0.4 1.0
N D:CYS40 4.7 90.2 1.0
CB D:GLU63 4.8 72.5 1.0
CA D:CYS149 4.8 73.5 1.0
HA D:CYS149 4.9 98.7 1.0
CG D:GLN88 5.0 87.1 1.0
HB2 D:GLU63 5.0 0.9 1.0

Zinc binding site 8 out of 8 in 5k1s

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Zinc binding site 8 out of 8 in the Crystal Structure of Aibc


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 Aibc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:0.5
occ:1.00
HG D:CYS98 2.0 0.9 1.0
SG D:CYS95 2.3 0.1 1.0
SG D:CYS98 2.4 0.1 1.0
HG D:CYS106 2.5 0.4 1.0
H D:CYS95 2.7 0.6 1.0
SG D:CYS106 2.8 0.4 1.0
SG D:CYS92 2.8 0.2 1.0
HB3 D:CYS92 2.9 0.7 1.0
H D:GLY93 3.0 0.5 1.0
HB3 D:CYS95 3.0 0.8 1.0
HB2 D:CYS106 3.0 0.4 1.0
HG D:CYS92 3.1 0.2 1.0
CB D:CYS95 3.2 0.4 1.0
CB D:CYS92 3.3 0.8 1.0
H D:ASP94 3.4 0.0 1.0
N D:CYS95 3.4 0.2 1.0
H D:CYS92 3.4 0.8 1.0
CB D:CYS106 3.5 0.9 1.0
HB2 D:CYS98 3.6 0.2 1.0
N D:GLY93 3.6 98.5 1.0
CB D:CYS98 3.7 0.1 1.0
N D:CYS92 3.9 0.5 1.0
CA D:CYS95 3.9 0.3 1.0
CA D:CYS92 4.0 0.7 1.0
HG1 D:THR108 4.0 0.2 1.0
HB2 D:CYS95 4.0 0.8 1.0
N D:ASP94 4.0 0.5 1.0
H D:CYS98 4.1 0.6 1.0
HB3 D:CYS106 4.1 0.4 1.0
C D:CYS92 4.1 0.8 1.0
HB2 D:CYS92 4.2 0.7 1.0
HB3 D:CYS98 4.3 0.2 1.0
OG D:SER91 4.4 0.6 1.0
HA D:CYS106 4.4 0.6 1.0
OG1 D:THR108 4.5 0.1 1.0
CA D:GLY93 4.5 97.4 1.0
C D:ASP94 4.5 0.2 1.0
C D:CYS95 4.6 0.7 1.0
CA D:CYS106 4.6 0.4 1.0
C D:GLY93 4.6 97.9 1.0
HA2 D:GLY93 4.7 0.7 1.0
N D:CYS98 4.7 1.0 1.0
HA D:CYS95 4.7 0.1 1.0
HA D:ASN103 4.8 0.2 1.0
O D:CYS95 4.8 0.9 1.0
CA D:CYS98 4.8 0.4 1.0
HG D:SER91 4.8 0.3 1.0
C D:SER91 4.8 0.3 1.0
HA D:CYS92 4.9 0.6 1.0
CA D:ASP94 4.9 0.3 1.0
HA D:SER91 4.9 0.5 1.0

Reference:

T.Bock, R.Muller, W.Blankenfeldt. Crystal Structure of Aibc, A Reductase Involved in Alternative De Novo Isovaleryl Coenzyme A Biosynthesis in Myxococcus Xanthus. Acta Crystallogr.,Sect.F V. 72 652 2016.
ISSN: ESSN 2053-230X
PubMed: 27487931
DOI: 10.1107/S2053230X16011146
Page generated: Wed Dec 16 06:26:10 2020

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