Atomistry » Sodium » PDB 4coo-4ddo » 4dd8
Atomistry »
  Sodium »
    PDB 4coo-4ddo »
      4dd8 »

Sodium 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
Calcium (Ca) 4 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Adam-8 Metalloproteinase Domain with Bound Batimastat (pdb code 4dd8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Adam-8 Metalloproteinase Domain with Bound Batimastat, PDB code: 4dd8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4dd8

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1003

b:13.6
occ:1.00
O A:ILE368 2.4 16.7 1.0
O A:HOH1103 2.4 16.8 1.0
O A:SER371 2.5 16.4 1.0
O A:HOH1104 2.6 14.8 1.0
O A:HOH1105 2.6 17.8 1.0
C A:ILE368 3.5 22.7 1.0
C A:SER371 3.7 18.5 1.0
CB A:ARG361 3.8 20.2 1.0
OE1 A:GLU358 3.9 18.5 1.0
CD A:PRO373 4.0 12.8 1.0
CD A:ARG361 4.0 17.3 1.0
OG A:SER371 4.1 27.1 1.0
N A:PRO373 4.1 18.1 1.0
CA A:ILE368 4.1 18.1 1.0
OE2 A:GLU358 4.2 16.7 1.0
C A:PHE372 4.4 18.2 1.0
CD A:GLU358 4.5 21.3 1.0
CA A:PRO373 4.5 15.6 1.0
CB A:PRO373 4.5 11.5 1.0
CG A:ARG361 4.5 20.2 1.0
O A:SER367 4.5 20.9 1.0
CG2 A:ILE368 4.5 14.8 1.0
CA A:SER371 4.5 18.7 1.0
N A:SER371 4.6 20.0 1.0
N A:PHE372 4.6 18.1 1.0
N A:GLY369 4.7 13.7 1.0
CA A:PHE372 4.7 15.6 1.0
CG A:PRO373 4.7 13.9 1.0
CB A:SER371 4.8 20.9 1.0
O A:HOH1112 4.9 14.7 1.0
O A:PHE372 4.9 19.7 1.0
CA A:GLY369 4.9 23.9 1.0
O A:ARG361 5.0 14.4 1.0
CB A:ILE368 5.0 13.0 1.0

Sodium binding site 2 out of 8 in 4dd8

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1005

b:45.5
occ:1.00
O A:GLY298 2.4 38.3 1.0
O A:HOH1106 2.5 28.5 1.0
OD1 A:ASP295 2.5 37.6 1.0
O A:PHE296 2.5 35.4 1.0
CG A:ASP295 3.0 38.5 1.0
OD2 A:ASP295 3.0 35.4 1.0
O A:HOH1133 3.6 29.1 1.0
C A:GLY298 3.7 32.9 1.0
C A:PHE296 3.8 32.8 1.0
N A:PHE296 4.2 28.3 1.0
C A:ASP295 4.3 28.8 1.0
N A:GLY298 4.3 27.4 1.0
CB A:ASP295 4.3 32.4 1.0
C A:THR297 4.5 32.7 1.0
CA A:THR299 4.6 32.9 1.0
N A:THR299 4.6 28.8 1.0
CA A:PHE296 4.6 34.2 1.0
CA A:GLY298 4.6 38.1 1.0
O A:ASP295 4.6 27.5 1.0
OE1 A:GLN319 4.6 32.1 1.0
NE2 A:GLN319 4.7 21.9 1.0
O A:THR300 4.7 25.8 1.0
CA A:ASP295 4.7 31.6 1.0
N A:THR297 4.8 31.1 1.0
CA A:THR297 4.9 38.4 1.0
O A:THR297 4.9 35.1 1.0
C A:THR299 5.0 28.0 1.0

Sodium binding site 3 out of 8 in 4dd8

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1003

b:18.5
occ:1.00
O B:HOH1102 2.5 16.3 1.0
O B:HOH1103 2.5 29.8 1.0
O B:HOH1104 2.5 19.9 1.0
O B:SER371 2.5 23.9 1.0
O B:ILE368 2.5 22.1 1.0
C B:ILE368 3.7 26.8 1.0
C B:SER371 3.7 19.9 1.0
N B:PRO373 4.1 16.2 1.0
OE2 B:GLU358 4.1 26.8 1.0
CD B:PRO373 4.1 18.9 1.0
CB B:ARG361 4.1 19.4 1.0
OE1 B:GLU358 4.2 20.0 1.0
CA B:ILE368 4.3 21.4 1.0
C B:PHE372 4.4 20.4 1.0
CB B:PRO373 4.4 20.2 1.0
CA B:PRO373 4.4 15.0 1.0
CD B:ARG361 4.4 30.0 1.0
NH1 B:ARG361 4.5 26.5 1.0
O B:SER367 4.5 21.5 1.0
CD B:GLU358 4.5 21.6 1.0
CA B:SER371 4.6 19.2 1.0
N B:SER371 4.6 21.0 1.0
N B:PHE372 4.7 20.3 1.0
O B:ARG361 4.7 19.7 1.0
CG B:PRO373 4.7 16.9 1.0
CA B:PHE372 4.7 18.6 1.0
CB B:SER371 4.7 24.6 1.0
N B:GLY369 4.7 22.4 1.0
CG2 B:ILE368 4.7 18.6 1.0
NE B:ARG361 4.8 29.4 1.0
CZ B:ARG361 4.8 35.6 1.0
O B:PHE372 4.9 21.6 1.0
CG B:ARG361 4.9 24.4 1.0
C B:ARG361 5.0 24.5 1.0
CA B:GLY369 5.0 21.5 1.0

Sodium binding site 4 out of 8 in 4dd8

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1005

b:34.8
occ:1.00
OD1 B:ASP295 2.4 27.5 1.0
O B:PHE296 2.5 29.3 1.0
O B:GLY298 2.5 30.4 1.0
O B:HOH1105 2.5 31.1 1.0
O B:HOH1106 2.5 33.9 1.0
OD2 B:ASP295 3.0 34.2 1.0
CG B:ASP295 3.0 34.3 1.0
O B:HOH1185 3.5 36.9 1.0
C B:GLY298 3.7 27.4 1.0
C B:PHE296 3.7 32.6 1.0
O B:HOH1164 4.1 29.0 1.0
N B:GLY298 4.2 29.3 1.0
N B:PHE296 4.3 26.6 1.0
C B:ASP295 4.4 26.3 1.0
CB B:ASP295 4.4 23.6 1.0
C B:THR297 4.5 32.1 1.0
CA B:PHE296 4.6 27.3 1.0
CA B:GLY298 4.6 30.2 1.0
N B:THR299 4.6 28.2 1.0
CA B:THR299 4.6 25.9 1.0
NE2 B:GLN319 4.7 14.8 1.0
N B:THR297 4.7 31.7 1.0
O B:ASP295 4.7 24.6 1.0
CA B:THR297 4.8 31.3 1.0
CA B:ASP295 4.8 25.9 1.0
OE1 B:GLN319 4.9 25.6 1.0
O B:THR300 5.0 24.9 1.0

Sodium binding site 5 out of 8 in 4dd8

Go back to Sodium Binding Sites List in 4dd8
Sodium binding site 5 out of 8 in the Adam-8 Metalloproteinase Domain with Bound Batimastat


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1003

b:18.6
occ:1.00
O C:ILE368 2.4 18.6 1.0
O C:SER371 2.4 20.6 1.0
O C:HOH1102 2.4 14.8 1.0
O C:HOH1104 2.4 26.4 1.0
O C:HOH1103 2.5 20.2 1.0
C C:ILE368 3.5 25.8 1.0
C C:SER371 3.6 19.9 1.0
OE2 C:GLU358 3.7 32.6 1.0
CD C:PRO373 4.0 20.2 1.0
N C:PRO373 4.0 20.6 1.0
CB C:ARG361 4.1 22.2 1.0
CA C:ILE368 4.2 25.4 1.0
CD C:ARG361 4.2 33.6 1.0
C C:PHE372 4.3 25.6 1.0
CA C:PRO373 4.5 18.1 1.0
N C:SER371 4.5 16.1 1.0
CG2 C:ILE368 4.5 22.9 1.0
OE1 C:GLU358 4.5 23.6 1.0
CB C:PRO373 4.5 19.2 1.0
CD C:GLU358 4.5 22.8 1.0
N C:PHE372 4.5 19.0 1.0
CA C:PHE372 4.6 19.8 1.0
O C:SER367 4.6 30.3 1.0
CA C:SER371 4.6 16.7 1.0
OG C:SER371 4.6 21.9 1.0
O C:HOH1117 4.6 25.6 1.0
N C:GLY369 4.6 22.9 1.0
CG C:ARG361 4.7 27.7 1.0
CG C:PRO373 4.7 15.4 1.0
O C:PHE372 4.9 20.8 1.0
CA C:GLY369 4.9 21.6 1.0
O C:ARG361 5.0 26.0 1.0
CB C:ILE368 5.0 17.8 1.0

Sodium binding site 6 out of 8 in 4dd8

Go back to Sodium Binding Sites List in 4dd8
Sodium binding site 6 out of 8 in the Adam-8 Metalloproteinase Domain with Bound Batimastat


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1005

b:39.1
occ:1.00
OD1 C:ASP295 2.4 33.2 1.0
O C:PHE296 2.4 26.4 1.0
O C:GLY298 2.5 24.9 1.0
O C:HOH1105 2.5 21.3 1.0
CG C:ASP295 3.0 35.4 1.0
OD2 C:ASP295 3.1 43.2 1.0
C C:PHE296 3.6 28.9 1.0
C C:GLY298 3.7 21.2 1.0
O C:HOH1159 3.9 31.7 1.0
N C:GLY298 4.2 29.3 1.0
N C:PHE296 4.2 31.1 1.0
O B:HOH1184 4.3 23.0 1.0
C C:ASP295 4.3 30.0 1.0
CB C:ASP295 4.4 25.8 1.0
C C:THR297 4.4 28.0 1.0
CA C:PHE296 4.5 32.8 1.0
CA C:GLY298 4.5 28.2 1.0
N C:THR299 4.6 29.1 1.0
N C:THR297 4.6 27.1 1.0
CA C:THR299 4.7 23.1 1.0
O C:ASP295 4.7 30.9 1.0
CA C:THR297 4.7 34.5 1.0
CA C:ASP295 4.8 28.8 1.0
NE2 C:GLN319 4.9 21.9 1.0
NH1 B:ARG277 4.9 41.3 1.0
O C:THR297 4.9 34.5 1.0
O C:THR300 4.9 26.4 1.0

Sodium binding site 7 out of 8 in 4dd8

Go back to Sodium Binding Sites List in 4dd8
Sodium binding site 7 out of 8 in the Adam-8 Metalloproteinase Domain with Bound Batimastat


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1003

b:17.2
occ:1.00
O D:HOH1105 2.4 23.0 1.0
O D:ILE368 2.4 21.9 1.0
O D:SER371 2.4 22.8 1.0
O D:HOH1106 2.5 18.6 1.0
O D:HOH1104 2.5 24.1 1.0
C D:ILE368 3.5 28.8 1.0
NH1 D:ARG361 3.6 26.2 1.0
C D:SER371 3.7 20.4 1.0
CG D:PRO373 3.9 18.7 1.0
OG D:SER371 4.0 26.1 1.0
N D:PRO373 4.0 20.1 1.0
CD D:PRO373 4.1 22.1 1.0
CA D:ILE368 4.1 25.2 1.0
C D:PHE372 4.3 23.0 1.0
OE2 D:GLU358 4.4 24.0 1.0
CA D:PRO373 4.4 22.1 1.0
O D:SER367 4.4 28.0 1.0
CB D:PRO373 4.5 22.9 1.0
CG2 D:ILE368 4.5 21.2 1.0
CB D:ARG361 4.5 20.4 1.0
CA D:SER371 4.6 22.2 1.0
N D:SER371 4.6 22.3 1.0
N D:PHE372 4.6 19.4 1.0
CA D:PHE372 4.6 18.6 1.0
N D:GLY369 4.7 23.7 1.0
O D:HOH1207 4.7 26.8 1.0
O D:PHE372 4.8 23.5 1.0
O D:ARG361 4.8 31.5 1.0
OE1 D:GLU358 4.8 23.1 1.0
CZ D:ARG361 4.9 23.1 1.0
CB D:SER371 4.9 20.9 1.0
CD D:GLU358 4.9 23.1 1.0
CB D:ILE368 5.0 21.1 1.0
CA D:GLY369 5.0 26.2 1.0

Sodium binding site 8 out of 8 in 4dd8

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Adam-8 Metalloproteinase Domain with Bound Batimastat within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1005

b:40.7
occ:1.00
O D:GLY298 2.5 26.6 1.0
O D:HOH1109 2.5 29.6 1.0
O D:PHE296 2.5 28.3 1.0
O D:HOH1108 2.5 36.1 1.0
O D:HOH1107 2.5 34.8 1.0
OD1 D:ASP295 3.2 39.9 1.0
C D:GLY298 3.6 28.1 1.0
CG D:ASP295 3.6 34.9 1.0
OD2 D:ASP295 3.6 39.9 1.0
C D:PHE296 3.7 30.5 1.0
N D:PHE296 4.2 36.0 1.0
CA D:THR299 4.3 26.3 1.0
N D:GLY298 4.3 36.5 1.0
N D:THR299 4.4 28.8 1.0
CA D:PHE296 4.4 32.1 1.0
C D:THR297 4.5 34.8 1.0
O D:THR300 4.5 27.4 1.0
C D:ASP295 4.5 32.7 1.0
CA D:GLY298 4.6 30.5 1.0
OE1 D:GLN319 4.6 33.1 1.0
N D:THR297 4.7 30.1 1.0
C D:THR299 4.7 24.9 1.0
CA D:THR297 4.8 27.5 1.0
CB D:ASP295 4.8 26.1 1.0
CB D:PHE296 4.9 24.7 1.0
N D:THR300 4.9 29.9 1.0
O D:THR297 4.9 37.2 1.0
CA D:ASP295 5.0 28.3 1.0
O D:ASP295 5.0 29.5 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: Tue Dec 15 06:36:41 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy