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Zinc in PDB 6g5n: Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine

Protein crystallography data

The structure of Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine, PDB code: 6g5n was solved by R.P.H.Talon, T.Krojer, C.Tallant, G.Nunez-Alonso, M.Fairhead, A.Szykowska, P.Collins, N.M.Pearce, J.Ng, E.Maclean, N.Wright, A.Douangamath, J.Brandao-Neto, N.Burgess-Brown, K.Huber, S.Knapp, P.E.Brennan, C.H.Arrowsmith, A.M.Edwards, C.Bountra, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.49 / 1.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.879, 45.426, 83.477, 90.00, 102.14, 90.00
R / Rfree (%) 17.5 / 22

Other elements in 6g5n:

The structure of Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine (pdb code 6g5n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine, PDB code: 6g5n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6g5n

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Zinc binding site 1 out of 4 in the Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:27.3
occ:1.00
ND1 A:HIS725 2.2 25.3 1.0
SG A:CYS728 2.2 26.6 1.0
SG A:CYS708 2.3 27.8 1.0
SG A:CYS705 2.3 26.9 1.0
CB A:CYS705 3.0 25.8 1.0
CG A:HIS725 3.2 29.2 1.0
CE1 A:HIS725 3.2 33.6 1.0
CB A:CYS728 3.2 28.9 1.0
CB A:CYS708 3.4 25.1 1.0
CB A:HIS725 3.4 27.9 1.0
N A:CYS708 3.8 25.2 1.0
O A:HOH1206 4.0 52.4 1.0
CA A:CYS708 4.1 22.6 1.0
N A:HIS725 4.2 27.4 1.0
NE2 A:HIS725 4.3 34.5 1.0
CD2 A:HIS725 4.3 31.1 1.0
CA A:HIS725 4.4 27.4 1.0
O A:HOH1177 4.5 37.8 1.0
CA A:CYS705 4.5 29.5 1.0
CB A:VAL707 4.6 22.1 1.0
CA A:CYS728 4.6 23.1 1.0
C A:CYS708 4.8 30.4 1.0
C A:VAL707 4.9 29.9 1.0

Zinc binding site 2 out of 4 in 6g5n

Go back to Zinc Binding Sites List in 6g5n
Zinc binding site 2 out of 4 in the Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:37.5
occ:1.00
SG A:CYS720 2.2 37.2 1.0
SG A:CYS717 2.3 40.6 1.0
SG A:CYS745 2.4 41.6 1.0
SG A:CYS742 2.4 33.1 1.0
CB A:CYS720 3.2 42.0 1.0
CB A:CYS717 3.2 30.9 1.0
CB A:CYS745 3.5 36.4 1.0
CB A:CYS742 3.5 24.8 1.0
N A:CYS742 3.7 39.2 1.0
N A:CYS720 3.9 48.2 1.0
OG1 A:THR719 3.9 48.2 1.0
CA A:CYS720 4.1 45.4 1.0
N A:CYS745 4.1 32.9 1.0
CA A:CYS742 4.1 37.6 1.0
CA A:CYS745 4.4 34.7 1.0
O A:CYS742 4.4 30.8 1.0
C A:THR719 4.5 45.1 1.0
C A:CYS742 4.6 34.7 1.0
C A:CYS720 4.6 36.5 1.0
NH1 A:ARG722 4.6 37.0 1.0
O A:CYS720 4.7 44.6 1.0
CA A:CYS717 4.7 40.8 1.0
O A:HOH1165 4.7 38.0 1.0
C A:SER741 4.8 39.5 1.0
CB A:PHE744 4.8 29.8 1.0
CB A:ARG722 4.9 38.0 1.0
N A:THR719 5.0 48.9 1.0
CB A:THR719 5.0 58.0 1.0

Zinc binding site 3 out of 4 in 6g5n

Go back to Zinc Binding Sites List in 6g5n
Zinc binding site 3 out of 4 in the Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:28.1
occ:1.00
ND1 B:HIS725 2.1 31.8 1.0
SG B:CYS728 2.3 24.3 1.0
SG B:CYS708 2.3 28.3 1.0
SG B:CYS705 2.3 26.8 1.0
CE1 B:HIS725 3.0 37.4 1.0
CB B:CYS705 3.0 28.6 1.0
CG B:HIS725 3.1 27.9 1.0
CB B:CYS728 3.1 25.7 1.0
CB B:CYS708 3.4 30.1 1.0
CB B:HIS725 3.4 26.9 1.0
N B:CYS708 3.8 26.7 1.0
O B:HOH1170 4.1 50.1 1.0
NE2 B:HIS725 4.1 36.2 1.0
CA B:CYS708 4.2 24.4 1.0
N B:HIS725 4.2 25.5 1.0
CD2 B:HIS725 4.2 35.3 1.0
CA B:HIS725 4.4 22.8 1.0
O B:HOH1148 4.5 54.7 1.0
CA B:CYS705 4.5 29.7 1.0
CA B:CYS728 4.6 22.9 1.0
O B:HOH1153 4.7 35.2 1.0
CB B:VAL707 4.7 27.2 1.0
C B:CYS708 4.9 34.2 1.0
C B:VAL707 4.9 27.1 1.0
N B:ASN709 5.0 30.4 1.0

Zinc binding site 4 out of 4 in 6g5n

Go back to Zinc Binding Sites List in 6g5n
Zinc binding site 4 out of 4 in the Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment XS039818E 1-(3-Phenyl-1,2,4-Oxadiazol-5-Yl)Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:33.9
occ:1.00
SG B:CYS720 2.3 38.1 1.0
SG B:CYS742 2.3 30.9 1.0
SG B:CYS717 2.3 35.3 1.0
SG B:CYS745 2.4 37.7 1.0
CB B:CYS717 3.2 31.4 1.0
CB B:CYS720 3.3 39.4 1.0
CB B:CYS742 3.4 28.5 1.0
CB B:CYS745 3.5 32.4 1.0
N B:CYS742 3.8 38.9 1.0
N B:CYS720 3.9 44.3 1.0
N B:CYS745 4.1 28.4 1.0
CA B:CYS720 4.1 43.5 1.0
CA B:CYS742 4.1 28.6 1.0
OG1 B:THR719 4.1 41.4 1.0
CA B:CYS745 4.3 33.0 1.0
C B:THR719 4.4 38.6 1.0
O B:CYS742 4.5 29.0 1.0
C B:CYS742 4.5 28.1 1.0
C B:CYS720 4.6 42.2 1.0
CA B:CYS717 4.7 33.1 1.0
O B:CYS720 4.7 40.7 1.0
O B:HOH1138 4.8 42.1 1.0
NH1 B:ARG722 4.8 37.9 1.0
CB B:PHE744 4.9 28.0 1.0
N B:THR719 4.9 43.1 1.0
C B:SER741 4.9 38.4 1.0
O B:THR719 4.9 45.9 1.0
CB B:ARG722 5.0 33.4 1.0

Reference:

R.P.H.Talon, D.Bowkett, C.Tallant, C.Schofield, F.Von Delft, S.Knapp, G.Bruton, P.E.Brennan. Identifying Small Molecule Binding Sites For Epigenetic Proteins at Domain-Domain Interfaces Biorxiv 2018.
DOI: 10.1101/283069
Page generated: Wed Dec 16 11:50:47 2020

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