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Zinc in PDB 2ch9: Crystal Structure of Dimeric Human Cystatin F

Protein crystallography data

The structure of Crystal Structure of Dimeric Human Cystatin F, PDB code: 2ch9 was solved by A.W.Schuettelkopf, D.M.F.Van Aalten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 65.345, 65.345, 123.183, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dimeric Human Cystatin F (pdb code 2ch9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Dimeric Human Cystatin F, PDB code: 2ch9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 2ch9

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Zinc binding site 1 out of 5 in the Crystal Structure of Dimeric Human Cystatin F


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 Dimeric Human Cystatin F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1155

b:56.1
occ:1.00
ND1 A:HIS147 2.1 55.8 1.0
NE2 A:HIS145 2.1 50.1 1.0
O A:HOH2058 2.2 55.8 1.0
CE1 A:HIS147 3.0 57.6 1.0
CD2 A:HIS145 3.0 50.9 1.0
CE1 A:HIS145 3.0 48.9 1.0
CG A:HIS147 3.1 57.1 1.0
CB A:HIS147 3.5 57.3 1.0
CA A:HIS147 4.0 57.8 1.0
NE2 A:HIS147 4.1 57.3 1.0
ND1 A:HIS145 4.1 50.2 1.0
CG A:HIS145 4.1 51.1 1.0
CD2 A:HIS147 4.2 56.8 1.0
N A:HIS147 4.7 56.5 1.0

Zinc binding site 2 out of 5 in 2ch9

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Zinc binding site 2 out of 5 in the Crystal Structure of Dimeric Human Cystatin F


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 Dimeric Human Cystatin F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1156

b:65.8
occ:0.75
NE2 A:HIS149 2.0 67.0 1.0
NE2 A:HIS146 2.0 60.3 1.0
O A:HOH2059 2.2 64.4 1.0
CE1 A:HIS149 2.7 67.3 1.0
CE1 A:HIS146 2.9 59.0 1.0
CD2 A:HIS146 3.1 57.4 1.0
CD2 A:HIS149 3.2 66.8 1.0
ND1 A:HIS149 3.9 67.5 1.0
ND1 A:HIS146 4.1 58.5 1.0
CG A:HIS149 4.2 66.6 1.0
CG A:HIS146 4.2 56.4 1.0
O A:LYS119 4.4 60.8 1.0
O A:HIS147 4.5 59.3 1.0
CA A:GLN120 4.5 59.0 1.0
NE2 A:GLN120 4.6 64.1 1.0
CG A:GLN120 4.6 60.6 1.0
N A:THR121 4.8 57.0 1.0
CB A:GLN120 4.8 59.2 1.0

Zinc binding site 3 out of 5 in 2ch9

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Zinc binding site 3 out of 5 in the Crystal Structure of Dimeric Human Cystatin F


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 Dimeric Human Cystatin F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1157

b:61.6
occ:0.70
O A:HOH2060 1.9 72.9 1.0
ND1 A:HIS104 2.1 51.2 1.0
O A:HOH2061 2.1 61.9 1.0
O A:HOH2062 2.2 60.7 1.0
CE1 A:HIS104 3.0 51.8 1.0
CG A:HIS104 3.1 50.0 1.0
CB A:HIS104 3.5 49.3 1.0
CA A:HIS104 4.0 49.5 1.0
O A:HOH2044 4.0 52.2 1.0
NE2 A:HIS104 4.1 50.3 1.0
CD2 A:HIS104 4.2 49.5 1.0
N A:HIS104 4.9 49.0 1.0

Zinc binding site 4 out of 5 in 2ch9

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Zinc binding site 4 out of 5 in the Crystal Structure of Dimeric Human Cystatin F


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 Dimeric Human Cystatin F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1158

b:68.3
occ:0.65
ND1 A:HIS136 2.1 61.1 1.0
O A:HOH2063 2.2 67.2 1.0
O A:HOH2064 2.2 66.6 1.0
CE1 A:HIS136 2.9 59.5 1.0
CG A:HIS136 3.1 59.0 1.0
CB A:HIS136 3.6 57.4 1.0
CA A:HIS136 3.8 57.0 1.0
NE2 A:HIS136 4.0 61.1 1.0
CD2 A:HIS136 4.1 60.0 1.0
N A:PHE137 4.3 56.2 1.0
O A:PHE137 4.3 54.4 1.0
O A:GLN135 4.5 57.3 1.0
C A:HIS136 4.6 56.6 1.0
N A:HIS136 4.9 57.2 1.0

Zinc binding site 5 out of 5 in 2ch9

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Zinc binding site 5 out of 5 in the Crystal Structure of Dimeric Human Cystatin F


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 Dimeric Human Cystatin F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1159

b:66.0
occ:0.50
OD2 A:ASP111 2.0 62.9 1.0
OD1 A:ASP111 2.0 61.7 1.0
O A:HOH2065 2.2 65.9 1.0
CG A:ASP111 2.3 59.8 1.0
CB A:ASP111 3.8 58.6 1.0
CA A:ASP111 4.7 58.2 1.0
N A:ASP111 5.0 58.0 1.0

Reference:

A.W.Schuttelkopf, G.Hamilton, C.Watts, D.M.F.Van Aalten. Structural Basis of Reduction-Dependent Activation of Human Cystatin F. J.Biol.Chem. V. 281 16570 2006.
ISSN: ISSN 0021-9258
PubMed: 16601115
DOI: 10.1074/JBC.M601033200
Page generated: Wed Dec 16 03:19:15 2020

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