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Zinc in PDB 2clt: Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.

Enzymatic activity of Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.

All present enzymatic activity of Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.:
3.4.24.7;

Protein crystallography data

The structure of Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase., PDB code: 2clt was solved by S.Iyer, R.Visse, H.Nagase, K.R.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.64 / 2.67
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 138.485, 138.485, 110.046, 90.00, 90.00, 120.00
R / Rfree (%) 22.3 / 25.9

Other elements in 2clt:

The structure of Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase. also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase. (pdb code 2clt). 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 the Active Form (Full-Length) of Human Fibroblast Collagenase., PDB code: 2clt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2clt

Go back to Zinc Binding Sites List in 2clt
Zinc binding site 1 out of 4 in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.


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 the Active Form (Full-Length) of Human Fibroblast Collagenase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1201

b:40.0
occ:1.00
 OD2 A:ASP151 2.1 66.5 1.0
ND1 A:HIS177 2.1 23.4 1.0
NE2 A:HIS149 2.2 56.4 1.0
NE2 A:HIS164 2.2 29.4 1.0
CE1 A:HIS149 2.8 55.0 1.0
CE1 A:HIS177 3.0 24.3 1.0
CG A:ASP151 3.1 67.4 1.0
CG A:HIS177 3.1 24.8 1.0
CD2 A:HIS164 3.1 31.9 1.0
CE1 A:HIS164 3.2 31.2 1.0
CD2 A:HIS149 3.3 55.2 1.0
OD1 A:ASP151 3.5 68.8 1.0
CB A:HIS177 3.5 23.1 1.0
ND1 A:HIS149 4.0 54.8 1.0
NE2 A:HIS177 4.1 25.3 1.0
CB A:SER153 4.1 66.3 1.0
CD2 A:HIS177 4.2 25.1 1.0
CE1 A:PHE166 4.2 36.8 1.0
O A:SER153 4.2 64.5 1.0
CG A:HIS149 4.3 56.3 1.0
CG A:HIS164 4.3 31.3 1.0
ND1 A:HIS164 4.3 32.3 1.0
CB A:ASP151 4.3 67.2 1.0
CZ A:PHE166 4.4 36.3 1.0
CE2 A:PHE155 4.8 50.1 1.0
C A:SER153 4.9 63.6 1.0
CG2 A:VAL145 4.9 35.4 1.0
CZ A:PHE155 4.9 50.1 1.0
CA A:HIS177 5.0 24.9 1.0
CA A:SER153 5.0 65.0 1.0

Zinc binding site 2 out of 4 in 2clt

Go back to Zinc Binding Sites List in 2clt
Zinc binding site 2 out of 4 in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.


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 the Active Form (Full-Length) of Human Fibroblast Collagenase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1202

b:29.4
occ:1.00
 NE2 A:HIS203 2.1 21.7 1.0
NE2 A:HIS199 2.2 25.1 1.0
NE2 A:HIS209 2.2 29.2 1.0
O A:HOH2106 2.3 16.0 1.0
CD2 A:HIS199 3.0 23.0 1.0
CE1 A:HIS203 3.1 24.9 1.0
CD2 A:HIS209 3.1 28.4 1.0
CD2 A:HIS203 3.2 24.9 1.0
CE1 A:HIS209 3.2 27.9 1.0
CE1 A:HIS199 3.3 23.4 1.0
ND1 A:HIS203 4.2 26.2 1.0
CG A:HIS199 4.2 24.0 1.0
CG A:HIS209 4.2 27.6 1.0
ND1 A:HIS209 4.3 30.0 1.0
CG A:HIS203 4.3 23.5 1.0
ND1 A:HIS199 4.3 25.1 1.0
O A:HOH2042 4.7 18.0 1.0
CE A:MET217 4.8 26.9 1.0
O A:HOH2038 4.9 35.6 1.0

Zinc binding site 3 out of 4 in 2clt

Go back to Zinc Binding Sites List in 2clt
Zinc binding site 3 out of 4 in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.


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 the Active Form (Full-Length) of Human Fibroblast Collagenase. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1401

b:36.4
occ:1.00
 ND1 B:HIS177 2.1 22.5 1.0
NE2 B:HIS164 2.2 32.5 1.0
OD2 B:ASP151 2.2 54.0 1.0
NE2 B:HIS149 2.3 54.2 1.0
CE1 B:HIS164 3.0 33.3 1.0
CE1 B:HIS177 3.1 24.0 1.0
CG B:HIS177 3.1 27.2 1.0
CG B:ASP151 3.1 54.0 1.0
CD2 B:HIS149 3.2 54.1 1.0
CD2 B:HIS164 3.2 33.1 1.0
CE1 B:HIS149 3.3 53.9 1.0
CB B:HIS177 3.4 28.0 1.0
OD1 B:ASP151 3.7 53.5 1.0
CB B:ASP151 4.1 55.1 1.0
ND1 B:HIS164 4.2 33.8 1.0
NE2 B:HIS177 4.2 24.4 1.0
CD2 B:HIS177 4.2 24.6 1.0
CG B:HIS149 4.3 55.1 1.0
CG B:HIS164 4.3 34.2 1.0
ND1 B:HIS149 4.3 54.4 1.0
O B:SER153 4.4 63.9 1.0
CZ B:PHE166 4.6 33.8 1.0
CE1 B:PHE166 4.6 33.3 1.0
CE2 B:PHE155 4.7 48.3 1.0
CG2 B:VAL145 4.8 35.1 1.0
CZ B:PHE155 4.8 46.2 1.0
CB B:SER153 4.9 66.4 1.0
CA B:HIS177 5.0 30.4 1.0

Zinc binding site 4 out of 4 in 2clt

Go back to Zinc Binding Sites List in 2clt
Zinc binding site 4 out of 4 in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.


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 the Active Form (Full-Length) of Human Fibroblast Collagenase. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1402

b:34.8
occ:1.00
 NE2 B:HIS209 2.0 33.6 1.0
NE2 B:HIS199 2.2 16.5 1.0
NE2 B:HIS203 2.2 16.2 1.0
O B:HOH2092 2.3 21.5 1.0
CD2 B:HIS209 3.0 34.1 1.0
CD2 B:HIS199 3.0 18.1 1.0
CE1 B:HIS209 3.0 34.5 1.0
CD2 B:HIS203 3.1 18.4 1.0
CE1 B:HIS203 3.2 17.8 1.0
CE1 B:HIS199 3.3 18.3 1.0
O B:HOH2028 3.7 42.0 1.0
ND1 B:HIS209 4.1 34.6 1.0
CG B:HIS209 4.1 33.0 1.0
CG B:HIS199 4.2 18.4 1.0
CG B:HIS203 4.3 20.0 1.0
ND1 B:HIS203 4.3 21.7 1.0
ND1 B:HIS199 4.3 17.9 1.0
O B:HOH2035 4.5 33.7 1.0
CE B:MET217 4.6 26.3 1.0
O B:HOH2038 4.7 29.3 1.0

Reference:

S.Iyer, R.Visse, H.Nagase, K.R.Acharya. Crystal Structure of An Active Form of Human Mmp-1. J.Mol.Biol. V. 362 78 2006.
ISSN: ISSN 0022-2836
PubMed: 16890240
DOI: 10.1016/J.JMB.2006.06.079
Page generated: Wed Oct 16 22:26:10 2024

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