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Zinc in PDB 4auo: Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide

Enzymatic activity of Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide

All present enzymatic activity of Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide:
3.4.24.7;

Protein crystallography data

The structure of Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide, PDB code: 4auo was solved by S.W.Manka, F.Carafoli, R.Visse, D.Bihan, N.Raynal, R.W.Farndale, G.Murphy, J.J.Enghild, E.Hohenester, H.Nagase, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20 / 3.00
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 76.671, 102.241, 80.734, 90.00, 103.75, 90.00
R / Rfree (%) 21.11 / 27.27

Other elements in 4auo:

The structure of Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide (pdb code 4auo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide, PDB code: 4auo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4auo

Go back to Zinc Binding Sites List in 4auo
Zinc binding site 1 out of 4 in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide


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 Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1201

b:35.2
occ:1.00
 NE2 A:HIS164 2.0 19.2 1.0
OD2 A:ASP151 2.1 45.0 1.0
ND1 A:HIS177 2.2 23.7 1.0
NE2 A:HIS149 2.2 34.5 1.0
CE1 A:HIS164 2.5 19.6 1.0
CG A:ASP151 2.7 44.1 1.0
CD2 A:HIS149 3.0 34.7 1.0
OD1 A:ASP151 3.0 44.5 1.0
CG A:HIS177 3.1 23.7 1.0
CE1 A:HIS177 3.1 23.1 1.0
CE1 A:HIS149 3.2 34.7 1.0
CD2 A:HIS164 3.3 18.4 1.0
CB A:HIS177 3.4 22.6 1.0
ND1 A:HIS164 3.8 17.9 1.0
CB A:ASP151 3.9 42.4 1.0
O A:SER153 4.0 29.4 1.0
CG A:HIS149 4.2 35.7 1.0
CG A:HIS164 4.2 17.6 1.0
ND1 A:HIS149 4.2 34.8 1.0
NE2 A:HIS177 4.2 24.1 1.0
CD2 A:HIS177 4.3 24.4 1.0
CE2 A:PHE155 4.3 19.9 1.0
CZ A:PHE166 4.5 16.6 1.0
CG2 A:VAL145 4.7 32.0 1.0
CZ A:PHE155 4.8 18.3 1.0
CE2 A:PHE166 4.8 17.4 1.0
C A:SER153 4.9 30.8 1.0
CB A:SER153 4.9 33.4 1.0
CA A:HIS177 4.9 22.2 1.0

Zinc binding site 2 out of 4 in 4auo

Go back to Zinc Binding Sites List in 4auo
Zinc binding site 2 out of 4 in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide


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 Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1202

b:23.1
occ:1.00
 NE2 A:HIS199 1.8 9.7 1.0
NE2 A:HIS203 1.9 14.0 1.0
NE2 A:HIS209 2.2 17.3 1.0
CD2 A:HIS199 2.8 10.3 1.0
CE1 A:HIS199 2.9 8.7 1.0
CD2 A:HIS203 2.9 15.1 1.0
CE1 A:HIS203 3.0 13.6 1.0
CD2 A:HIS209 3.1 17.4 1.0
CE1 A:HIS209 3.3 16.9 1.0
CG A:HIS199 3.9 10.4 1.0
ND1 A:HIS199 3.9 8.8 1.0
CG A:HIS203 4.0 16.2 1.0
ND1 A:HIS203 4.0 16.6 1.0
CG A:HIS209 4.3 17.3 1.0
ND1 A:HIS209 4.3 16.2 1.0

Zinc binding site 3 out of 4 in 4auo

Go back to Zinc Binding Sites List in 4auo
Zinc binding site 3 out of 4 in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide


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 Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:25.5
occ:1.00
 NE2 B:HIS164 1.8 13.5 1.0
ND1 B:HIS177 2.0 18.9 1.0
OD2 B:ASP151 2.0 34.3 1.0
NE2 B:HIS149 2.4 32.7 1.0
CE1 B:HIS164 2.5 11.4 1.0
CG B:ASP151 2.7 35.4 1.0
CE1 B:HIS177 2.9 21.9 1.0
CD2 B:HIS149 3.0 34.0 1.0
CG B:HIS177 3.0 19.0 1.0
OD1 B:ASP151 3.0 35.3 1.0
CD2 B:HIS164 3.1 13.2 1.0
CB B:HIS177 3.4 18.4 1.0
CE1 B:HIS149 3.5 33.4 1.0
ND1 B:HIS164 3.8 11.5 1.0
CB B:ASP151 3.8 35.8 1.0
NE2 B:HIS177 4.0 22.4 1.0
CG B:HIS164 4.0 12.7 1.0
CD2 B:HIS177 4.1 20.8 1.0
CG B:HIS149 4.2 35.4 1.0
O B:SER153 4.3 34.9 1.0
CZ B:PHE166 4.3 22.1 1.0
CE1 B:PHE166 4.4 21.9 1.0
ND1 B:HIS149 4.5 35.1 1.0
CE2 B:PHE155 4.6 19.1 1.0
CZ B:PHE155 4.9 17.8 1.0
CB B:SER153 4.9 36.9 1.0
CG2 B:VAL145 4.9 28.3 1.0
CA B:HIS177 4.9 17.3 1.0

Zinc binding site 4 out of 4 in 4auo

Go back to Zinc Binding Sites List in 4auo
Zinc binding site 4 out of 4 in the Crystal Structure of Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide


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 Mmp-1(E200A) in Complex with A Triple- Helical Collagen Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1202

b:20.4
occ:1.00
 NE2 B:HIS199 1.9 17.1 1.0
NE2 B:HIS203 2.0 11.8 1.0
NE2 B:HIS209 2.2 15.2 1.0
CE1 B:HIS199 2.9 16.5 1.0
CD2 B:HIS203 2.9 11.5 1.0
CE1 B:HIS203 3.0 12.3 1.0
CD2 B:HIS199 3.0 16.7 1.0
CD2 B:HIS209 3.0 14.7 1.0
CE1 B:HIS209 3.2 15.2 1.0
ND1 B:HIS199 4.0 16.9 1.0
CG B:HIS203 4.0 11.7 1.0
ND1 B:HIS203 4.0 12.9 1.0
CG B:HIS199 4.1 17.6 1.0
CG B:HIS209 4.2 15.9 1.0
CD1 F:LEU976 4.3 30.8 1.0
ND1 B:HIS209 4.3 14.5 1.0
CG F:LEU976 4.8 30.4 1.0

Reference:

S.W.Manka, F.Carafoli, R.Visse, D.Bihan, N.Raynal, R.W.Farndale, G.Murphy, J.J.Enghild, E.Hohenester, H.Nagase. Structural Insights Into Triple-Helical Collagen Cleavage By Matrix Metalloproteinase 1 Proc.Natl.Acad.Sci.Usa V. 109 12461 2012.
ISSN: ISSN 0027-8424
PubMed: 22761315
DOI: 10.1073/PNAS.1204991109
Page generated: Sat Oct 26 19:23:24 2024

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