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Zinc in PDB 1cxv: Structure of Recombinant Mouse Collagenase-3 (Mmp-13)

Protein crystallography data

The structure of Structure of Recombinant Mouse Collagenase-3 (Mmp-13), PDB code: 1cxv was solved by I.Botos, E.Meyer, S.M.Swanson, V.Lemaitre, Y.Eeckhout, E.F.Meyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.360, 48.460, 74.940, 90.00, 108.15, 90.00
R / Rfree (%) 19.6 / 23.4

Other elements in 1cxv:

The structure of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13) (pdb code 1cxv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13), PDB code: 1cxv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1cxv

Go back to Zinc Binding Sites List in 1cxv
Zinc binding site 1 out of 4 in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:20.4
occ:1.00
NE2 A:HIS201 2.0 20.0 1.0
NE2 A:HIS205 2.0 19.1 1.0
NE2 A:HIS211 2.1 20.6 1.0
O1 A:CBP10 2.1 21.6 1.0
O4 A:CBP10 2.6 23.6 1.0
N2 A:CBP10 2.7 25.8 1.0
CD2 A:HIS201 2.9 19.1 1.0
CD2 A:HIS205 3.0 17.7 1.0
C3 A:CBP10 3.1 25.2 1.0
CD2 A:HIS211 3.1 20.8 1.0
CE1 A:HIS211 3.1 20.8 1.0
CE1 A:HIS201 3.1 19.7 1.0
CE1 A:HIS205 3.1 18.3 1.0
O A:HOH849 3.9 18.7 1.0
CG A:HIS201 4.1 19.1 1.0
ND1 A:HIS201 4.2 19.4 1.0
CG A:HIS205 4.2 16.9 1.0
CG A:HIS211 4.2 21.1 1.0
OE2 A:GLU202 4.2 18.9 1.0
ND1 A:HIS211 4.2 20.3 1.0
ND1 A:HIS205 4.3 17.1 1.0
C5 A:CBP10 4.6 26.0 1.0
C16 A:CBP10 4.7 26.4 1.0
C17 A:CBP10 4.7 26.0 1.0
CE A:MET219 4.9 19.6 1.0
CD A:GLU202 4.9 18.1 1.0
OE1 A:GLU202 5.0 17.3 1.0

Zinc binding site 2 out of 4 in 1cxv

Go back to Zinc Binding Sites List in 1cxv
Zinc binding site 2 out of 4 in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:23.7
occ:1.00
ND1 A:HIS179 2.0 22.4 1.0
NE2 A:HIS151 2.0 24.5 1.0
OD2 A:ASP153 2.0 25.5 1.0
NE2 A:HIS166 2.0 21.6 1.0
CD2 A:HIS151 2.9 25.6 1.0
CG A:ASP153 2.9 26.7 1.0
CE1 A:HIS179 3.0 22.1 1.0
CE1 A:HIS166 3.0 21.8 1.0
CG A:HIS179 3.0 21.7 1.0
CD2 A:HIS166 3.0 21.7 1.0
CE1 A:HIS151 3.1 25.2 1.0
OD1 A:ASP153 3.2 25.9 1.0
CB A:HIS179 3.4 20.9 1.0
O A:TYR155 4.1 32.2 1.0
CG A:HIS151 4.1 26.5 1.0
CD2 A:HIS179 4.1 21.9 1.0
NE2 A:HIS179 4.1 22.2 1.0
ND1 A:HIS166 4.1 21.6 1.0
ND1 A:HIS151 4.2 26.0 1.0
CG A:HIS166 4.2 21.2 1.0
CB A:ASP153 4.3 28.2 1.0
CZ A:PHE168 4.5 23.1 1.0
CB A:TYR155 4.6 34.6 1.0
CZ A:PHE157 4.6 28.3 1.0
CE2 A:PHE157 4.7 28.6 1.0
CE1 A:PHE168 4.7 23.1 1.0
CA A:HIS179 4.9 20.1 1.0
C A:TYR155 4.9 32.2 1.0

Zinc binding site 3 out of 4 in 1cxv

Go back to Zinc Binding Sites List in 1cxv
Zinc binding site 3 out of 4 in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:20.4
occ:1.00
NE2 B:HIS501 2.0 20.2 1.0
NE2 B:HIS505 2.0 19.1 1.0
NE2 B:HIS511 2.0 20.8 1.0
O1 B:CBP11 2.1 21.9 1.0
O4 B:CBP11 2.6 23.4 1.0
N2 B:CBP11 2.7 25.9 1.0
CD2 B:HIS501 2.9 19.3 1.0
CD2 B:HIS505 3.0 17.5 1.0
CD2 B:HIS511 3.0 21.0 1.0
CE1 B:HIS511 3.1 21.1 1.0
C3 B:CBP11 3.1 25.2 1.0
CE1 B:HIS505 3.1 17.9 1.0
CE1 B:HIS501 3.1 20.2 1.0
CG B:HIS501 4.1 18.8 1.0
O B:HOH759 4.1 27.2 1.0
OE2 B:GLU502 4.2 18.9 1.0
CG B:HIS505 4.2 16.8 1.0
ND1 B:HIS501 4.2 19.5 1.0
CG B:HIS511 4.2 21.2 1.0
ND1 B:HIS511 4.2 20.8 1.0
ND1 B:HIS505 4.2 16.7 1.0
C5 B:CBP11 4.6 26.3 1.0
C16 B:CBP11 4.7 26.3 1.0
C17 B:CBP11 4.7 26.3 1.0
O B:HOH738 4.8 48.2 1.0
CE B:MET519 4.8 19.5 1.0
CD B:GLU502 5.0 18.1 1.0

Zinc binding site 4 out of 4 in 1cxv

Go back to Zinc Binding Sites List in 1cxv
Zinc binding site 4 out of 4 in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:23.1
occ:1.00
OD2 B:ASP453 1.9 24.9 1.0
NE2 B:HIS451 2.0 24.3 1.0
NE2 B:HIS466 2.0 21.6 1.0
ND1 B:HIS479 2.1 22.1 1.0
CG B:ASP453 2.8 26.5 1.0
CD2 B:HIS451 2.9 25.4 1.0
CE1 B:HIS466 3.0 21.9 1.0
CE1 B:HIS451 3.0 24.8 1.0
CE1 B:HIS479 3.0 22.1 1.0
OD1 B:ASP453 3.1 25.6 1.0
CD2 B:HIS466 3.1 21.8 1.0
CG B:HIS479 3.1 21.5 1.0
CB B:HIS479 3.5 20.6 1.0
CG B:HIS451 4.1 26.4 1.0
ND1 B:HIS451 4.1 25.7 1.0
O B:TYR455 4.1 32.5 1.0
ND1 B:HIS466 4.2 21.3 1.0
CD2 B:HIS479 4.2 21.6 1.0
NE2 B:HIS479 4.2 22.1 1.0
CG B:HIS466 4.2 21.1 1.0
CB B:ASP453 4.2 27.8 1.0
CZ B:PHE468 4.4 23.3 1.0
CE1 B:PHE468 4.7 23.3 1.0
CZ B:PHE457 4.7 28.1 1.0
CE2 B:PHE457 4.7 28.6 1.0
O B:HOH622 5.0 24.8 1.0
C B:TYR455 5.0 32.7 1.0
CB B:TYR455 5.0 35.8 1.0
CA B:HIS479 5.0 20.2 1.0

Reference:

I.Botos, E.Meyer, S.M.Swanson, V.Lemaitre, Y.Eeckhout, E.F.Meyer. Structure of Recombinant Mouse Collagenase-3 (Mmp-13). J.Mol.Biol. V. 292 837 1999.
ISSN: ISSN 0022-2836
PubMed: 10525409
DOI: 10.1006/JMBI.1999.3068
Page generated: Mon Jan 25 16:08:08 2021

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