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Calcium in PDB 1rm8: Crystal Structure of the Catalytic Domain of Mmp-16/MT3-Mmp: Characterization of Mt-Mmp Specific Features

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-16/MT3-Mmp: Characterization of Mt-Mmp Specific Features, PDB code: 1rm8 was solved by R.Lang, M.Braun, N.E.Sounni, A.Noel, F.Frankenne, J.-M.Foidart, W.Bode, K.Maskos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.60 / 1.80
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 51.210, 51.210, 149.368, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.6

Other elements in 1rm8:

The structure of Crystal Structure of the Catalytic Domain of Mmp-16/MT3-Mmp: Characterization of Mt-Mmp Specific Features also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Mmp-16/MT3-Mmp: Characterization of Mt-Mmp Specific Features (pdb code 1rm8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Mmp-16/MT3-Mmp: Characterization of Mt-Mmp Specific Features, PDB code: 1rm8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1rm8

Go back to Calcium Binding Sites List in 1rm8
Calcium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Mmp-16/MT3-Mmp: Characterization of Mt-Mmp Specific Features


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 Catalytic Domain of Mmp-16/MT3-Mmp: Characterization of Mt-Mmp Specific Features within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:21.5
occ:1.00
OE1 A:GLU226 2.1 26.1 1.0
O A:GLY201 2.3 30.1 1.0
O A:GLY203 2.3 28.0 1.0
OD1 A:ASP223 2.3 20.6 1.0
OD1 A:ASP200 2.3 22.8 1.0
O A:PHE205 2.4 19.1 1.0
CD A:GLU226 3.4 24.2 1.0
CG A:ASP223 3.4 20.8 1.0
C A:GLY201 3.5 29.5 1.0
C A:GLY203 3.5 28.4 1.0
CG A:ASP200 3.5 26.1 1.0
C A:PHE205 3.5 20.9 1.0
N A:GLY203 3.8 28.9 1.0
OD2 A:ASP200 4.0 28.5 1.0
OE2 A:GLU226 4.0 26.3 1.0
CB A:ASP223 4.0 19.5 1.0
N A:PHE205 4.0 23.7 1.0
N A:GLY201 4.1 28.3 1.0
C A:GLU202 4.1 30.0 1.0
CA A:GLY203 4.2 29.3 1.0
C A:ASP200 4.2 28.1 1.0
N A:ASP200 4.3 24.4 1.0
CA A:GLY201 4.4 29.9 1.0
OD2 A:ASP223 4.4 19.2 1.0
C A:GLY204 4.4 25.3 1.0
CA A:PHE205 4.4 22.6 1.0
N A:GLU202 4.4 30.4 1.0
CA A:GLU202 4.4 30.7 1.0
N A:LEU206 4.4 18.8 1.0
CG A:GLU226 4.5 23.4 1.0
CA A:LEU206 4.5 18.7 1.0
N A:GLY204 4.5 26.7 1.0
O A:ASP200 4.7 28.5 1.0
CA A:ASP200 4.7 26.3 1.0
CB A:ASP200 4.7 26.9 1.0
O A:GLU202 4.7 29.1 1.0
O A:HOH1041 4.7 35.6 1.0
CA A:GLY204 4.7 26.4 1.0
O A:GLY204 4.9 25.9 1.0
CD2 A:LEU206 4.9 23.0 1.0

Calcium binding site 2 out of 2 in 1rm8

Go back to Calcium Binding Sites List in 1rm8
Calcium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Mmp-16/MT3-Mmp: Characterization of Mt-Mmp Specific Features


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 Catalytic Domain of Mmp-16/MT3-Mmp: Characterization of Mt-Mmp Specific Features within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:39.1
occ:1.00
OD2 A:ASP219 2.3 20.5 1.0
O A:GLY217 2.3 20.0 1.0
O A:GLY215 2.3 23.4 1.0
O A:HOH1076 2.4 19.1 1.0
O A:ASP183 2.4 24.9 1.0
O A:HOH1023 3.2 24.6 1.0
CG A:ASP219 3.3 21.1 1.0
C A:GLY217 3.4 21.1 1.0
C A:ASP183 3.5 23.2 1.0
C A:GLY215 3.5 23.1 1.0
O A:HOH1077 3.5 34.2 1.0
C A:ILE216 3.6 21.8 1.0
O A:HOH1078 3.7 26.6 1.0
OD1 A:ASP219 3.8 20.7 1.0
N A:GLY217 3.8 21.0 1.0
O A:ILE216 3.8 20.6 1.0
CA A:ILE216 3.9 22.4 1.0
N A:ASP219 4.0 18.0 1.0
O A:HOH1115 4.0 28.4 1.0
CA A:ILE184 4.1 20.4 1.0
N A:ILE216 4.1 22.9 1.0
N A:ILE184 4.2 22.0 1.0
CA A:GLY217 4.2 21.0 1.0
N A:THR185 4.3 21.1 1.0
O A:VAL182 4.3 28.5 1.0
N A:GLY218 4.4 18.5 1.0
CB A:ASP219 4.5 18.7 1.0
C A:GLY218 4.5 17.7 1.0
CA A:GLY218 4.5 18.6 1.0
CA A:ASP183 4.5 25.1 1.0
CA A:ASP219 4.6 18.2 1.0
OG1 A:THR185 4.6 21.7 1.0
C A:ILE184 4.6 21.1 1.0
CA A:GLY215 4.7 23.8 1.0
O A:GLY213 4.8 20.2 1.0
N A:GLY215 4.9 24.0 1.0

Reference:

R.Lang, M.Braun, N.E.Sounni, A.Noel, F.Frankenne, J.M.Foidart, W.Bode, K.Maskos. Crystal Structure of the Catalytic Domain of Mmp-16/MT3-Mmp: Characterization of Mt-Mmp Specific Features. J.Mol.Biol. V. 336 213 2004.
ISSN: ISSN 0022-2836
PubMed: 14741217
DOI: 10.1016/J.JMB.2003.12.022
Page generated: Sat Dec 12 03:17:55 2020

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