Atomistry » Calcium » PDB 2c5d-2cn3 » 2clt
Atomistry »
  Calcium »
    PDB 2c5d-2cn3 »
      2clt »

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

Go back to Calcium Binding Sites List in 2clt
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

Go back to Calcium Binding Sites List in 2clt
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

Go back to Calcium Binding Sites List in 2clt
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

Go back to Calcium Binding Sites List in 2clt
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

Go back to Calcium Binding Sites List in 2clt
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

Go back to Calcium Binding Sites List in 2clt
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

Go back to Calcium Binding Sites List in 2clt
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

Go back to Calcium Binding Sites List in 2clt
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: Tue Jul 8 04:51:43 2025

Last articles

Mg in 4WFM
Mg in 4WFL
Mg in 4WCE
Mg in 4WF7
Mg in 4WEC
Mg in 4WEO
Mg in 4WCW
Mg in 4WE1
Mg in 4WCU
Mg in 4WDQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy