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Zinc in PDB 4g9i: Crystal Structure of T.Kodakarensis Hypf

Protein crystallography data

The structure of Crystal Structure of T.Kodakarensis Hypf, PDB code: 4g9i was solved by T.Tominaga, S.Watanabe, R.Matsumi, H.Atomi, T.Imanaka, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 4.50
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 265.810, 265.810, 693.712, 90.00, 90.00, 120.00
R / Rfree (%) 27.9 / 30

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of T.Kodakarensis Hypf (pdb code 4g9i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Crystal Structure of T.Kodakarensis Hypf, PDB code: 4g9i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in 4g9i

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Zinc binding site 1 out of 18 in the Crystal Structure of T.Kodakarensis Hypf


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 T.Kodakarensis Hypf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:0.1
occ:1.00
 SG A:CYS134 2.6 0.7 1.0
SG A:CYS112 2.6 0.5 1.0
SG A:CYS131 2.7 1.0 1.0
SG A:CYS109 2.7 0.8 1.0
CB A:CYS112 3.1 0.6 1.0
CB A:CYS131 3.1 0.7 1.0
N A:CYS131 3.2 0.1 1.0
CB A:CYS109 3.2 0.4 1.0
N A:CYS109 3.6 0.3 1.0
CA A:CYS131 3.7 0.2 1.0
CB A:CYS134 3.8 0.4 1.0
CA A:CYS109 4.0 0.0 1.0
C A:VAL130 4.0 0.9 1.0
CA A:CYS112 4.3 0.5 1.0
CA A:VAL130 4.3 0.5 1.0
N A:CYS112 4.3 0.4 1.0
O A:CYS109 4.5 0.4 1.0
C A:CYS131 4.5 0.4 1.0
N A:CYS134 4.7 0.7 1.0
C A:CYS109 4.7 0.2 1.0
C A:ILE108 4.7 0.7 1.0
CG2 A:ILE108 4.8 0.3 1.0
O A:CYS131 4.8 0.1 1.0
CA A:CYS134 4.8 1.0 1.0
CA A:ILE108 5.0 0.1 1.0
C A:ASN133 5.0 0.1 1.0
O A:VAL130 5.0 0.8 1.0

Zinc binding site 2 out of 18 in 4g9i

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Zinc binding site 2 out of 18 in the Crystal Structure of T.Kodakarensis Hypf


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 T.Kodakarensis Hypf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:0.5
occ:1.00
 CB A:CYS181 2.5 0.3 1.0
SG A:CYS184 2.6 0.2 1.0
SG A:CYS162 2.6 0.2 1.0
SG A:CYS159 2.7 0.1 1.0
SG A:CYS181 2.9 0.9 1.0
N A:CYS181 3.3 0.2 1.0
CA A:CYS181 3.4 0.1 1.0
C A:ALA180 3.6 0.7 1.0
CG2 A:VAL183 3.7 0.0 1.0
CB A:CYS159 3.7 0.5 1.0
CB A:CYS162 3.9 0.7 1.0
O A:ALA180 3.9 0.6 1.0
CB A:CYS184 4.0 0.2 1.0
N A:CYS184 4.1 0.1 1.0
C A:CYS181 4.2 1.0 1.0
CA A:ALA180 4.2 0.3 1.0
N A:CYS159 4.3 0.7 1.0
O A:CYS181 4.4 0.8 1.0
CA A:CYS184 4.6 0.7 1.0
CA A:CYS159 4.6 0.1 1.0
N A:CYS162 4.6 0.9 1.0
N A:GLY185 4.8 0.6 1.0
CA A:CYS162 4.8 0.6 1.0
O A:CYS159 4.9 0.2 1.0
N A:VAL183 4.9 1.0 1.0
CB A:VAL183 5.0 0.3 1.0

Zinc binding site 3 out of 18 in 4g9i

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Zinc binding site 3 out of 18 in the Crystal Structure of T.Kodakarensis Hypf


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 T.Kodakarensis Hypf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:0.2
occ:1.00
 NE2 A:HIS490 2.0 0.5 1.0
OD1 A:ASP746 2.0 0.4 1.0
NE2 A:HIS486 2.3 0.7 1.0
OD2 A:ASP509 2.3 0.6 1.0
CE1 A:HIS490 2.6 0.5 1.0
CG A:ASP509 2.6 0.1 1.0
OD1 A:ASP509 2.6 0.1 1.0
CG A:ASP746 2.8 0.5 1.0
CE1 A:HIS486 3.0 0.2 1.0
CD2 A:HIS490 3.2 0.0 1.0
OD2 A:ASP746 3.2 0.6 1.0
CD2 A:HIS486 3.4 0.6 1.0
ND1 A:HIS490 3.7 0.9 1.0
CB A:ASP509 3.8 0.1 1.0
CB A:ASP746 3.9 0.1 1.0
CA A:ASP746 4.0 0.5 1.0
N A:GLY714 4.0 0.8 1.0
CG A:HIS490 4.0 0.6 1.0
ND1 A:HIS486 4.2 0.5 1.0
N A:ASP746 4.3 0.8 1.0
CG A:HIS486 4.4 0.5 1.0
CA A:GLY714 4.6 0.3 1.0
C A:GLY713 4.8 0.2 1.0
CA A:GLY713 4.8 0.4 1.0
CA A:ASP509 4.9 0.8 1.0

Zinc binding site 4 out of 18 in 4g9i

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Zinc binding site 4 out of 18 in the Crystal Structure of T.Kodakarensis Hypf


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 T.Kodakarensis Hypf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:0.1
occ:1.00
 CB B:CYS112 2.7 0.4 1.0
SG B:CYS134 2.7 0.7 1.0
SG B:CYS131 2.7 1.0 1.0
SG B:CYS109 2.9 0.3 1.0
SG B:CYS112 3.0 0.5 1.0
CB B:CYS131 3.4 0.6 1.0
N B:CYS109 3.6 0.0 1.0
CB B:CYS134 3.7 0.3 1.0
N B:CYS131 3.8 0.6 1.0
CA B:CYS112 3.9 0.7 1.0
CB B:CYS109 4.0 0.0 1.0
N B:CYS112 4.1 0.5 1.0
CA B:CYS131 4.2 0.2 1.0
NH2 B:ARG172 4.3 0.3 1.0
CA B:CYS109 4.3 0.1 1.0
O B:CYS109 4.4 1.0 1.0
CA B:ILE108 4.5 0.3 1.0
C B:ILE108 4.5 0.7 1.0
N B:CYS134 4.6 0.4 1.0
CA B:CYS134 4.7 0.9 1.0
C B:VAL130 4.7 0.6 1.0
C B:CYS109 4.8 0.8 1.0
CB B:ILE108 4.8 0.2 1.0
C B:ASN133 4.9 0.2 1.0
C B:CYS131 4.9 0.9 1.0
CA B:VAL130 5.0 0.2 1.0
C B:CYS112 5.0 0.1 1.0

Zinc binding site 5 out of 18 in 4g9i

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Zinc binding site 5 out of 18 in the Crystal Structure of T.Kodakarensis Hypf


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 T.Kodakarensis Hypf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:0.1
occ:1.00
 CB B:CYS181 2.8 0.3 1.0
SG B:CYS184 2.8 0.7 1.0
SG B:CYS162 2.9 0.5 1.0
SG B:CYS159 2.9 1.0 1.0
N B:CYS181 3.3 0.4 1.0
CG2 B:VAL183 3.3 0.1 1.0
SG B:CYS181 3.3 0.7 1.0
CA B:CYS181 3.5 0.8 1.0
C B:ALA180 3.8 0.4 1.0
CB B:CYS162 3.8 0.8 1.0
CB B:CYS159 4.1 0.1 1.0
C B:CYS181 4.2 0.4 1.0
N B:CYS184 4.3 0.2 1.0
O B:CYS181 4.3 0.5 1.0
CA B:ALA180 4.3 0.9 1.0
O B:ALA180 4.3 0.9 1.0
CB B:CYS184 4.4 0.4 1.0
N B:CYS162 4.6 0.7 1.0
CA B:CYS162 4.7 0.8 1.0
CB B:VAL183 4.7 0.6 1.0
N B:CYS159 4.7 0.7 1.0
CA B:CYS184 4.9 0.6 1.0
N B:VAL183 4.9 0.6 1.0
CA B:CYS159 5.0 0.7 1.0

Zinc binding site 6 out of 18 in 4g9i

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Zinc binding site 6 out of 18 in the Crystal Structure of T.Kodakarensis Hypf


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 T.Kodakarensis Hypf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:0.1
occ:1.00
 OD1 B:ASP746 2.2 0.0 1.0
NE2 B:HIS486 2.2 1.0 1.0
NE2 B:HIS490 2.4 0.2 1.0
OD1 B:ASP509 2.4 0.9 1.0
CG B:ASP746 2.8 0.5 1.0
CE1 B:HIS486 2.8 0.2 1.0
CG B:ASP509 2.8 0.6 1.0
OD2 B:ASP509 3.0 0.9 1.0
CD2 B:HIS490 3.0 0.8 1.0
OD2 B:ASP746 3.1 0.7 1.0
CD2 B:HIS486 3.5 0.9 1.0
CE1 B:HIS490 3.5 0.3 1.0
CB B:ASP746 3.9 0.4 1.0
CB B:ASP509 3.9 0.4 1.0
CA B:ASP746 4.0 0.9 1.0
ND1 B:HIS486 4.1 0.9 1.0
CG B:HIS490 4.3 0.8 1.0
N B:ASP746 4.4 0.1 1.0
CG B:HIS486 4.4 1.0 1.0
N B:GLY714 4.5 0.3 1.0
ND1 B:HIS490 4.5 0.7 1.0
CA B:ASP509 5.0 0.7 1.0

Zinc binding site 7 out of 18 in 4g9i

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Zinc binding site 7 out of 18 in the Crystal Structure of T.Kodakarensis Hypf


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 T.Kodakarensis Hypf within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:0.3
occ:1.00
 SG C:CYS134 2.6 0.9 1.0
SG C:CYS112 2.7 0.8 1.0
SG C:CYS131 2.7 0.8 1.0
SG C:CYS109 2.9 0.9 1.0
CB C:CYS131 3.0 0.4 1.0
N C:CYS131 3.1 0.8 1.0
CB C:CYS112 3.1 0.7 1.0
CB C:CYS109 3.5 0.3 1.0
CB C:CYS134 3.5 0.8 1.0
CA C:CYS131 3.6 0.1 1.0
N C:CYS109 3.7 0.6 1.0
C C:VAL130 3.8 0.9 1.0
CA C:VAL130 4.1 0.5 1.0
CA C:CYS109 4.1 0.0 1.0
CA C:CYS112 4.4 0.6 1.0
N C:CYS112 4.4 0.1 1.0
O C:CYS109 4.5 0.9 1.0
C C:CYS131 4.5 0.9 1.0
N C:CYS134 4.6 0.1 1.0
CA C:CYS134 4.6 0.9 1.0
O C:VAL130 4.7 0.4 1.0
C C:CYS109 4.8 0.1 1.0
O C:CYS131 4.8 0.7 1.0
CG1 C:ILE108 4.8 0.8 1.0
C C:ILE108 4.8 0.4 1.0
C C:ASN133 4.9 0.2 1.0
N C:VAL130 5.0 0.3 1.0

Zinc binding site 8 out of 18 in 4g9i

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Zinc binding site 8 out of 18 in the Crystal Structure of T.Kodakarensis Hypf


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 T.Kodakarensis Hypf within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:0.2
occ:1.00
 CB C:CYS181 2.7 0.2 1.0
SG C:CYS159 2.7 0.0 1.0
SG C:CYS162 2.7 0.7 1.0
SG C:CYS184 2.9 0.9 1.0
N C:CYS181 3.1 0.2 1.0
SG C:CYS181 3.2 0.6 1.0
CG2 C:VAL183 3.3 0.1 1.0
CA C:CYS181 3.4 1.0 1.0
C C:ALA180 3.6 0.4 1.0
CB C:CYS159 3.7 0.5 1.0
CB C:CYS162 3.8 1.0 1.0
N C:CYS184 4.0 1.0 1.0
C C:CYS181 4.0 0.5 1.0
CA C:ALA180 4.1 0.8 1.0
CB C:CYS184 4.1 0.6 1.0
O C:CYS181 4.1 0.8 1.0
O C:ALA180 4.2 0.8 1.0
N C:CYS159 4.4 0.0 1.0
N C:CYS162 4.6 0.5 1.0
CB C:VAL183 4.7 0.4 1.0
CA C:CYS184 4.7 0.4 1.0
CA C:CYS159 4.7 0.1 1.0
N C:VAL183 4.7 0.7 1.0
CA C:CYS162 4.8 0.8 1.0
CB C:ALA180 4.9 0.9 1.0
CD2 C:PHE161 5.0 0.1 1.0

Zinc binding site 9 out of 18 in 4g9i

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Zinc binding site 9 out of 18 in the Crystal Structure of T.Kodakarensis Hypf


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 T.Kodakarensis Hypf within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1003

b:0.3
occ:1.00
 OD2 C:ASP509 2.1 0.4 1.0
NE2 C:HIS490 2.2 0.6 1.0
OD1 C:ASP746 2.3 0.8 1.0
NE2 C:HIS486 2.4 1.0 1.0
CG C:ASP746 2.6 0.4 1.0
OD2 C:ASP746 2.6 0.6 1.0
CG C:ASP509 2.8 0.5 1.0
CD2 C:HIS490 3.0 0.4 1.0
CE1 C:HIS486 3.0 0.6 1.0
OD1 C:ASP509 3.2 0.2 1.0
CE1 C:HIS490 3.4 0.6 1.0
CD2 C:HIS486 3.7 0.4 1.0
CB C:ASP746 3.9 0.6 1.0
CB C:ASP509 4.0 0.5 1.0
CA C:ASP746 4.0 0.3 1.0
CG C:HIS490 4.2 0.6 1.0
ND1 C:HIS486 4.3 0.7 1.0
ND1 C:HIS490 4.4 0.2 1.0
N C:ASP746 4.5 0.8 1.0
N C:GLY714 4.5 0.3 1.0
CG C:HIS486 4.6 0.0 1.0
CA C:GLY713 4.9 0.9 1.0

Zinc binding site 10 out of 18 in 4g9i

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Zinc binding site 10 out of 18 in the Crystal Structure of T.Kodakarensis Hypf


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 T.Kodakarensis Hypf within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:0.1
occ:1.00
 SG D:CYS134 2.7 0.6 1.0
SG D:CYS109 2.7 0.6 1.0
SG D:CYS112 2.7 0.3 1.0
SG D:CYS131 2.8 0.8 1.0
CB D:CYS112 2.9 0.8 1.0
N D:CYS131 3.2 0.1 1.0
CB D:CYS131 3.4 0.9 1.0
CB D:CYS109 3.5 0.5 1.0
N D:CYS109 3.6 0.1 1.0
CA D:CYS131 3.9 0.4 1.0
CB D:CYS134 4.0 0.4 1.0
CA D:CYS112 4.1 0.5 1.0
CA D:CYS109 4.1 0.4 1.0
C D:VAL130 4.1 0.9 1.0
CA D:VAL130 4.2 0.6 1.0
N D:CYS112 4.2 0.3 1.0
O D:CYS109 4.5 0.8 1.0
CG2 D:ILE108 4.6 0.4 1.0
C D:CYS131 4.7 0.1 1.0
NH2 D:ARG172 4.7 0.1 1.0
C D:CYS109 4.7 0.8 1.0
C D:ILE108 4.7 0.7 1.0
O D:CYS131 4.8 0.9 1.0
N D:CYS134 4.8 0.6 1.0
CA D:ILE108 4.9 0.2 1.0
CG2 D:VAL130 4.9 0.8 1.0
CZ D:ARG172 4.9 0.1 1.0
CA D:CYS134 4.9 0.4 1.0

Reference:

T.Tominaga, S.Watanabe, R.Matsumi, H.Atomi, T.Imanaka, K.Miki. Structure of the [Nife]-Hydrogenase Maturation Protein Hypf From Thermococcus Kodakarensis KOD1. Acta Crystallogr.,Sect.F V. 68 1153 2012.
ISSN: ESSN 1744-3091
PubMed: 23027738
DOI: 10.1107/S1744309112036421
Page generated: Sat Oct 26 23:10:26 2024

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