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Calcium in PDB 4dd8: Adam-8 Metalloproteinase Domain with Bound Batimastat

Protein crystallography data

The structure of Adam-8 Metalloproteinase Domain with Bound Batimastat, PDB code: 4dd8 was solved by T.Hall, H.S.Shieh, J.E.Day, N.Caspers, J.E.Chrencik, J.M.Williams, L.E.Pegg, A.M.Pauley, A.F.Moon, J.M.Krahn, D.H.Fischer, J.R.Kiefer, A.G.Tomasselli, M.D.Zack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.74 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.600, 50.900, 93.500, 90.00, 102.40, 90.00
R / Rfree (%) 18.8 / 25.5

Other elements in 4dd8:

The structure of Adam-8 Metalloproteinase Domain with Bound Batimastat also contains other interesting chemical elements:

Potassium (K) 2 atoms
Zinc (Zn) 4 atoms
Chlorine (Cl) 4 atoms
Sodium (Na) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Adam-8 Metalloproteinase Domain with Bound Batimastat (pdb code 4dd8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Adam-8 Metalloproteinase Domain with Bound Batimastat, PDB code: 4dd8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4dd8

Go back to Calcium Binding Sites List in 4dd8
Calcium binding site 1 out of 4 in the Adam-8 Metalloproteinase Domain with Bound Batimastat


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:20.6
occ:1.00
O A:CYS395 2.3 22.8 1.0
OD1 A:ASN398 2.3 25.1 1.0
O A:HOH1102 2.3 19.3 1.0
O A:HOH1101 2.4 18.4 1.0
OE1 A:GLU203 2.4 25.1 1.0
OD1 A:ASP286 2.4 19.4 1.0
OD2 A:ASP286 2.4 17.3 1.0
CG A:ASP286 2.7 23.6 1.0
ND2 A:ASN398 3.0 24.7 1.0
CG A:ASN398 3.0 26.5 1.0
CD A:GLU203 3.3 29.0 1.0
C A:CYS395 3.5 22.7 1.0
CG A:GLU203 3.8 25.5 1.0
CB A:ASP286 4.2 17.5 1.0
CA A:CYS395 4.2 23.8 1.0
CB A:CYS395 4.3 29.9 1.0
CB A:GLU203 4.3 23.3 1.0
OE2 A:GLU203 4.3 33.1 1.0
SG A:CYS395 4.4 51.7 1.0
O A:ASN398 4.4 23.6 1.0
O A:TYR201 4.4 21.1 1.0
CB A:ASN398 4.5 23.0 1.0
N A:LEU396 4.5 19.9 1.0
CA A:LEU396 4.6 24.7 1.0
N A:GLU203 4.8 17.6 1.0
N A:ASN398 4.9 22.3 1.0

Calcium binding site 2 out of 4 in 4dd8

Go back to Calcium Binding Sites List in 4dd8
Calcium binding site 2 out of 4 in the Adam-8 Metalloproteinase Domain with Bound Batimastat


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:24.2
occ:1.00
O B:HOH1101 2.3 25.8 1.0
OD2 B:ASP286 2.4 17.7 1.0
O B:CYS395 2.4 30.3 1.0
OE1 B:GLU203 2.4 41.5 1.0
OD1 B:ASP286 2.5 15.3 1.0
OD1 B:ASN398 2.5 29.9 1.0
CG B:ASP286 2.7 19.9 1.0
CD B:GLU203 3.3 40.3 1.0
C B:CYS395 3.6 25.6 1.0
CG B:ASN398 3.6 37.6 1.0
CG B:GLU203 3.8 25.9 1.0
O B:HOH1179 3.9 24.4 1.0
ND2 B:ASN398 4.0 44.2 1.0
OE2 B:GLU203 4.2 39.3 1.0
CB B:ASP286 4.3 17.1 1.0
CA B:CYS395 4.3 29.4 1.0
CB B:GLU203 4.3 14.8 1.0
O B:ASN398 4.4 34.2 1.0
CB B:CYS395 4.5 35.8 1.0
O B:TYR201 4.5 21.5 1.0
N B:LEU396 4.6 25.6 1.0
CA B:LEU396 4.8 24.7 1.0
N B:GLU203 4.8 19.3 1.0
CB B:ASN398 4.9 34.3 1.0
N B:ASN398 5.0 35.5 1.0

Calcium binding site 3 out of 4 in 4dd8

Go back to Calcium Binding Sites List in 4dd8
Calcium binding site 3 out of 4 in the Adam-8 Metalloproteinase Domain with Bound Batimastat


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1001

b:24.8
occ:1.00
O C:CYS395 2.3 29.4 1.0
OD1 C:ASN398 2.4 29.5 1.0
O C:HOH1101 2.4 16.2 1.0
OE1 C:GLU203 2.4 30.9 1.0
OD1 C:ASP286 2.4 20.9 1.0
OD2 C:ASP286 2.4 16.6 1.0
CG C:ASP286 2.7 22.5 1.0
CG C:ASN398 3.2 29.7 1.0
ND2 C:ASN398 3.3 26.7 1.0
CD C:GLU203 3.5 34.7 1.0
C C:CYS395 3.5 26.1 1.0
CG C:GLU203 4.0 30.1 1.0
CA C:CYS395 4.3 20.3 1.0
CB C:ASP286 4.3 23.4 1.0
CB C:CYS395 4.3 26.4 1.0
CB C:GLU203 4.4 24.5 1.0
OE2 C:GLU203 4.5 50.0 1.0
N C:LEU396 4.5 20.5 1.0
O C:ASN398 4.5 33.9 1.0
O C:TYR201 4.5 22.6 1.0
CB C:ASN398 4.6 25.4 1.0
CA C:LEU396 4.7 21.1 1.0
N C:GLU203 4.8 17.7 1.0
SG C:CYS395 4.8 39.1 1.0
N C:ASN398 5.0 26.8 1.0

Calcium binding site 4 out of 4 in 4dd8

Go back to Calcium Binding Sites List in 4dd8
Calcium binding site 4 out of 4 in the Adam-8 Metalloproteinase Domain with Bound Batimastat


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1001

b:31.7
occ:1.00
O D:HOH1103 2.3 24.2 1.0
O D:HOH1194 2.4 28.6 1.0
O D:CYS395 2.4 31.9 1.0
OE1 D:GLU203 2.4 39.0 1.0
OD1 D:ASN398 2.4 29.0 1.0
OD1 D:ASP286 2.5 27.0 1.0
OD2 D:ASP286 2.5 22.2 1.0
CG D:ASP286 2.8 26.4 1.0
CG D:ASN398 3.3 40.9 1.0
CD D:GLU203 3.4 38.6 1.0
ND2 D:ASN398 3.5 42.5 1.0
C D:CYS395 3.5 21.8 1.0
CG D:GLU203 3.8 28.9 1.0
CB D:CYS395 4.2 33.5 1.0
O D:HOH1160 4.2 22.3 1.0
CA D:CYS395 4.2 31.0 1.0
CB D:ASP286 4.3 16.6 1.0
CB D:GLU203 4.4 17.6 1.0
OE2 D:GLU203 4.4 34.7 1.0
SG D:CYS395 4.6 40.1 1.0
N D:LEU396 4.6 28.5 1.0
CB D:ASN398 4.7 34.0 1.0
O D:TYR201 4.7 24.3 1.0
CA D:LEU396 4.9 26.4 1.0
N D:GLU203 4.9 17.1 1.0
O D:ASN398 5.0 38.9 1.0

Reference:

T.Hall, H.S.Shieh, J.E.Day, N.Caspers, J.E.Chrencik, J.M.Williams, L.E.Pegg, A.M.Pauley, A.F.Moon, J.M.Krahn, D.H.Fischer, J.R.Kiefer, A.G.Tomasselli, M.D.Zack. Structure of Human Adam-8 Catalytic Domain Complexed with Batimastat. Acta Crystallogr.,Sect.F V. 68 616 2012.
ISSN: ESSN 1744-3091
PubMed: 22684055
DOI: 10.1107/S1744309112015618
Page generated: Sat Dec 12 04:43:23 2020

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