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Calcium 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:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase., PDB code: 2clt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2clt

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Calcium binding site 1 out of 8 in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1101

b:28.1
occ:1.00
 O A:GLU180 2.3 31.4 1.0
OE1 B:GLN335 2.3 44.4 1.0
OD2 A:ASP105 2.4 37.1 1.0
O A:GLU182 2.4 32.6 1.0
OE2 A:GLU180 2.5 31.2 1.0
O A:HOH2034 3.0 27.0 1.0
OD1 A:ASP105 3.1 36.2 1.0
CG A:ASP105 3.1 35.7 1.0
CD B:GLN335 3.3 39.1 1.0
C A:GLU180 3.5 33.5 1.0
C A:GLU182 3.5 33.3 1.0
CD A:GLU180 3.6 32.2 1.0
CG B:GLN335 3.6 38.0 1.0
NH2 A:ARG146 3.7 66.3 1.0
CG A:GLU180 4.0 29.8 1.0
N A:GLU182 4.2 33.2 1.0
OG1 A:THR103 4.3 38.3 1.0
CA A:ARG183 4.3 33.1 1.0
N A:ARG183 4.3 32.3 1.0
CA A:GLU180 4.3 32.4 1.0
N A:ASP181 4.4 32.5 1.0
NE2 B:GLN335 4.5 42.6 1.0
CA A:GLU182 4.5 34.0 1.0
CB B:GLN335 4.5 36.3 1.0
CA A:ASP181 4.5 34.3 1.0
C A:ASP181 4.5 33.4 1.0
CB A:ASP105 4.6 33.4 1.0
CD1 A:TRP184 4.6 22.4 1.0
OE1 A:GLU180 4.6 31.7 1.0
CB A:GLU180 4.8 31.6 1.0
N A:TRP184 4.9 29.5 1.0
CZ A:ARG146 4.9 65.9 1.0

Calcium binding site 2 out of 8 in 2clt

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Calcium binding site 2 out of 8 in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1102

b:45.8
occ:1.00
 O A:ASP266 2.3 32.8 1.0
O A:GLU310 2.3 38.2 1.0
O A:ASP359 2.5 53.5 1.0
O A:ASP408 2.7 34.4 1.0
C A:ASP266 3.4 30.4 1.0
C A:GLU310 3.4 38.7 1.0
C A:ASP359 3.5 54.3 1.0
C A:ASP408 3.8 35.8 1.0
CA A:GLU310 3.9 40.9 1.0
O A:HOH2079 3.9 41.5 1.0
CA A:ASP359 4.0 56.7 1.0
CA A:ASP266 4.0 31.1 1.0
CA A:ASP408 4.4 38.4 1.0
N A:ALA267 4.4 28.8 1.0
CB A:GLU310 4.5 43.9 1.0
N A:ALA311 4.6 35.5 1.0
N A:ALA360 4.7 51.2 1.0
O A:PHE265 4.7 31.0 1.0
CA A:ALA267 4.7 29.1 1.0
O A:ILE358 4.7 61.3 1.0
CB A:ASP359 4.7 58.8 1.0
CB A:ALA267 4.8 28.3 1.0
CB A:ASP266 4.9 32.4 1.0
N A:ALA409 4.9 32.4 1.0
CA A:ALA311 5.0 34.8 1.0
O A:VAL407 5.0 42.9 1.0

Calcium binding site 3 out of 8 in 2clt

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Calcium binding site 3 out of 8 in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
A:Ca1103

b:44.7
occ:1.00
 O A:GLY173 2.0 25.5 1.0
O A:GLY171 2.3 36.4 1.0
OD2 A:ASP175 2.3 47.5 1.0
O A:ASP139 2.4 33.0 1.0
O A:HOH2044 2.4 36.6 1.0
C A:GLY173 3.2 25.8 1.0
CG A:ASP175 3.5 42.7 1.0
C A:GLY171 3.5 34.1 1.0
N A:GLY173 3.6 29.7 1.0
C A:ASP139 3.6 33.7 1.0
C A:ILE172 3.8 30.8 1.0
CA A:GLY173 3.8 26.7 1.0
OD1 A:ASP175 4.0 47.1 1.0
O A:ALA138 4.1 42.1 1.0
O A:ILE172 4.1 31.9 1.0
N A:ASP175 4.2 30.7 1.0
O A:GLY169 4.2 39.4 1.0
N A:GLY174 4.2 27.1 1.0
CA A:ILE172 4.3 30.9 1.0
N A:ILE172 4.3 32.8 1.0
CA A:ASP139 4.4 34.9 1.0
CA A:GLY174 4.5 28.4 1.0
CH2 A:TRP90 4.5 24.4 1.0
CA A:GLY171 4.5 34.6 1.0
C A:GLY174 4.5 29.4 1.0
N A:ILE140 4.6 32.3 1.0
CB A:ASP175 4.7 36.6 1.0
CA A:ILE140 4.7 30.9 1.0
N A:GLY171 4.7 34.5 1.0
N A:MET141 4.8 33.1 1.0
CA A:ASP175 4.9 31.7 1.0
C A:PRO170 4.9 35.4 1.0
CG A:MET141 5.0 35.7 1.0

Calcium binding site 4 out of 8 in 2clt

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Calcium binding site 4 out of 8 in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
A:Ca1104

b:47.7
occ:1.00
 O A:GLY159 2.0 48.6 1.0
OD2 A:ASP156 2.3 54.4 1.0
OD2 A:ASP179 2.4 33.6 1.0
O A:GLY157 2.4 52.0 1.0
OE2 A:GLU182 2.4 44.0 1.0
O A:ASN161 2.6 45.9 1.0
C A:GLY159 3.2 48.2 1.0
CG A:ASP156 3.5 56.2 1.0
CG A:ASP179 3.5 33.9 1.0
C A:GLY157 3.6 51.3 1.0
C A:ASN161 3.6 44.4 1.0
CD A:GLU182 3.6 44.6 1.0
N A:ASN161 3.8 45.4 1.0
N A:GLY159 4.1 48.1 1.0
C A:ASP156 4.1 56.4 1.0
N A:GLY157 4.1 55.5 1.0
OD1 A:ASP156 4.1 57.2 1.0
N A:GLY160 4.1 47.7 1.0
CA A:GLY159 4.1 47.9 1.0
CB A:ASP179 4.2 32.4 1.0
C A:PRO158 4.2 47.9 1.0
CA A:ASN161 4.2 44.9 1.0
C A:GLY160 4.2 47.3 1.0
CA A:GLY160 4.3 47.3 1.0
N A:ASP156 4.3 56.1 1.0
O A:ASP156 4.3 57.0 1.0
CG A:GLU182 4.4 42.0 1.0
CA A:GLY157 4.4 53.5 1.0
O A:PRO158 4.5 48.0 1.0
N A:PRO158 4.5 50.0 1.0
CA A:ASP156 4.5 55.9 1.0
OD1 A:ASP179 4.5 37.3 1.0
CB A:ASP156 4.5 56.0 1.0
OE1 A:GLU182 4.6 45.0 1.0
N A:LEU162 4.6 40.3 1.0
CA A:PRO158 4.6 48.9 1.0
CA A:LEU162 4.9 38.3 1.0
CB A:ASN161 4.9 44.4 1.0

Calcium binding site 5 out of 8 in 2clt

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Calcium binding site 5 out of 8 in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 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:Ca1301

b:59.6
occ:1.00
 OE2 B:GLU180 2.1 43.1 1.0
O B:GLU180 2.3 36.4 1.0
O B:GLU182 2.4 39.0 1.0
OD2 B:ASP105 2.4 49.3 1.0
O A:HOH2084 2.8 60.0 1.0
CG B:ASP105 3.2 47.0 1.0
OD1 B:ASP105 3.3 49.2 1.0
CD B:GLU180 3.4 41.4 1.0
C B:GLU180 3.4 36.6 1.0
C B:GLU182 3.5 37.6 1.0
OG1 B:THR103 4.0 43.3 1.0
CG B:GLU180 4.1 38.6 1.0
CA B:GLU180 4.2 36.4 1.0
CA B:ARG183 4.2 37.2 1.0
N B:GLU182 4.2 38.2 1.0
CD1 B:TRP184 4.3 27.7 1.0
OE1 B:GLU180 4.3 42.1 1.0
N B:ARG183 4.3 37.7 1.0
N B:ASP181 4.4 37.6 1.0
NH1 A:ARG285 4.4 38.8 1.0
C B:ASP181 4.5 39.6 1.0
CA B:GLU182 4.5 37.4 1.0
N B:TRP184 4.6 33.9 1.0
CA B:ASP181 4.6 39.8 1.0
OE1 A:GLU294 4.6 49.2 1.0
CB B:ASP105 4.7 44.6 1.0
CB B:GLU180 4.8 35.3 1.0
CZ A:PHE301 4.8 48.0 1.0
NE1 B:TRP184 4.8 24.5 1.0
OE2 A:GLU294 4.9 48.5 1.0
C B:ARG183 5.0 35.8 1.0

Calcium binding site 6 out of 8 in 2clt

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Calcium binding site 6 out of 8 in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 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:Ca1302

b:57.7
occ:1.00
 O B:ASP266 2.3 48.2 1.0
O B:ASP359 2.4 53.6 1.0
O B:GLU310 2.4 51.9 1.0
O B:ASP408 2.4 54.9 1.0
C B:ASP359 3.5 53.7 1.0
C B:ASP266 3.5 47.2 1.0
C B:GLU310 3.5 50.5 1.0
C B:ASP408 3.6 54.8 1.0
CA B:GLU310 4.1 50.5 1.0
CA B:ASP359 4.1 53.4 1.0
CA B:ASP408 4.1 54.9 1.0
CA B:ASP266 4.2 49.2 1.0
N B:ALA267 4.5 44.7 1.0
N B:ALA360 4.5 53.8 1.0
N B:ALA311 4.6 50.6 1.0
O B:PHE265 4.6 48.4 1.0
CA B:ALA267 4.7 42.1 1.0
CB B:GLU310 4.7 49.8 1.0
N B:ALA409 4.7 54.4 1.0
CB B:ASP359 4.8 53.1 1.0
O B:VAL407 4.8 54.9 1.0
CA B:ALA360 4.9 55.2 1.0
CB B:ASP408 4.9 55.1 1.0
CA B:ALA311 4.9 50.7 1.0
CB B:ALA267 4.9 37.4 1.0
CB B:ALA360 4.9 54.2 1.0

Calcium binding site 7 out of 8 in 2clt

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Calcium binding site 7 out of 8 in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 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:Ca1303

b:64.3
occ:0.50
 O B:GLY173 2.1 38.7 1.0
O B:GLY171 2.3 42.6 1.0
O B:ASP139 2.3 34.9 1.0
O B:HOH2043 2.3 41.3 1.0
C B:GLY173 3.2 38.8 1.0
C B:ASP139 3.4 36.0 1.0
C B:GLY171 3.4 40.6 1.0
OD1 B:ASP175 3.6 41.0 1.0
O B:ALA138 3.7 43.0 1.0
CA B:ILE172 3.9 42.3 1.0
N B:GLY174 4.1 37.6 1.0
N B:GLY173 4.1 41.8 1.0
CG B:ASP175 4.1 39.8 1.0
CA B:GLY174 4.1 38.4 1.0
N B:ILE172 4.1 41.0 1.0
C B:ILE172 4.2 42.9 1.0
CA B:GLY173 4.2 40.1 1.0
CA B:ASP139 4.2 38.3 1.0
O B:GLY169 4.3 31.1 1.0
N B:ILE140 4.3 34.1 1.0
OD2 B:ASP175 4.4 41.2 1.0
N B:ASP175 4.4 37.0 1.0
CA B:ILE140 4.5 33.6 1.0
CH2 B:TRP90 4.6 33.5 1.0
CA B:GLY171 4.6 39.0 1.0
C B:GLY174 4.6 38.1 1.0
N B:MET141 4.7 33.3 1.0
C B:ALA138 4.7 43.9 1.0
CG B:MET141 4.9 38.2 1.0
O B:ILE172 4.9 46.8 1.0
N B:GLY171 5.0 36.7 1.0
N B:ASP139 5.0 40.4 1.0

Calcium binding site 8 out of 8 in 2clt

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Calcium binding site 8 out of 8 in the Crystal Structure of the Active Form (Full-Length) of Human Fibroblast Collagenase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 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:Ca1304

b:50.0
occ:1.00
 OE2 B:GLU182 2.2 36.8 1.0
O B:GLY159 2.3 47.2 1.0
OD2 B:ASP179 2.3 40.4 1.0
O B:ASN161 2.4 42.5 1.0
OD1 B:ASP156 2.4 49.8 1.0
O B:GLY157 2.5 51.3 1.0
CG B:ASP179 3.4 39.8 1.0
C B:GLY159 3.4 47.4 1.0
CD B:GLU182 3.5 37.1 1.0
C B:ASN161 3.5 41.1 1.0
CG B:ASP156 3.7 52.0 1.0
C B:GLY157 3.7 49.9 1.0
N B:ASP156 3.9 52.4 1.0
N B:ASN161 4.0 42.4 1.0
C B:ASP156 4.0 51.7 1.0
N B:GLY157 4.1 50.2 1.0
CB B:ASP179 4.2 37.4 1.0
N B:GLY159 4.2 47.2 1.0
C B:GLY160 4.2 43.6 1.0
CG B:GLU182 4.2 39.0 1.0
C B:PRO158 4.3 46.6 1.0
CA B:ASN161 4.3 42.0 1.0
O B:ASP156 4.3 52.1 1.0
N B:GLY160 4.3 46.9 1.0
OD1 B:ASP179 4.3 40.7 1.0
CA B:GLY160 4.3 44.9 1.0
CA B:ASP156 4.4 52.0 1.0
OE1 B:GLU182 4.4 36.4 1.0
CA B:GLY159 4.4 47.8 1.0
O B:PRO158 4.4 45.4 1.0
CA B:GLY157 4.5 49.9 1.0
OD2 B:ASP156 4.5 52.5 1.0
N B:LEU162 4.6 40.2 1.0
CB B:ASP156 4.6 51.7 1.0
N B:PRO158 4.7 49.3 1.0
CB B:PHE155 4.7 51.9 1.0
O B:HOH2045 4.7 33.1 1.0
CD1 B:PHE155 4.8 48.2 1.0
CB B:ASN161 4.8 42.9 1.0
CA B:PRO158 4.8 48.1 1.0
CA B:LEU162 4.8 39.0 1.0
O B:GLY160 4.9 42.3 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: Fri Jul 12 09:31:32 2024

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