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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Oct 7 14:52:59 2024

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