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Vanadium in PDB 3omx: Crystal Structure of SSU72 with Vanadate Complex

Protein crystallography data

The structure of Crystal Structure of SSU72 with Vanadate Complex, PDB code: 3omx was solved by Y.Zhang, M.Zhang, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.66 / 2.34
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 157.616, 102.309, 65.816, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26.7

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Crystal Structure of SSU72 with Vanadate Complex (pdb code 3omx). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 4 binding sites of Vanadium where determined in the Crystal Structure of SSU72 with Vanadate Complex, PDB code: 3omx:
Jump to Vanadium binding site number: 1; 2; 3; 4;

Vanadium binding site 1 out of 4 in 3omx

Go back to Vanadium Binding Sites List in 3omx
Vanadium binding site 1 out of 4 in the Crystal Structure of SSU72 with Vanadate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Crystal Structure of SSU72 with Vanadate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V300

b:48.6
occ:1.00
V A:VO4300 0.0 48.6 1.0
O4 A:VO4300 1.9 46.7 1.0
O2 A:VO4300 1.9 49.2 1.0
O3 A:VO4300 2.0 46.7 1.0
O1 A:VO4300 2.0 52.2 1.0
SG A:CYS13 2.3 43.0 1.0
CB A:CYS13 3.4 39.9 1.0
N A:ASN18 3.8 45.5 1.0
N A:ARG19 3.9 40.3 1.0
NE A:ARG19 3.9 38.8 1.0
N A:SER14 4.0 39.7 1.0
N A:SER15 4.0 40.9 1.0
NH2 A:ARG19 4.0 43.3 1.0
O A:HOH250 4.2 60.6 1.0
N A:ASN16 4.2 41.1 1.0
N A:MET17 4.3 43.0 1.0
CB A:SER15 4.3 42.9 1.0
CB A:ASN18 4.4 43.6 1.0
CA A:ASN18 4.4 43.1 1.0
CZ A:ARG19 4.5 42.2 1.0
CA A:SER15 4.5 47.2 1.0
C A:ASN18 4.6 43.7 1.0
CA A:CYS13 4.6 39.4 1.0
OD1 A:ASP144 4.6 52.0 1.0
OD2 A:ASP144 4.6 54.3 1.0
CB A:ARG19 4.7 37.2 1.0
C A:CYS13 4.7 41.4 1.0
C A:SER15 4.7 43.7 1.0
CG A:ASP144 4.8 55.2 1.0
CA A:SER14 4.8 45.9 1.0
N A:SER20 4.8 41.2 1.0
C A:MET17 4.8 44.4 1.0
CA A:ARG19 4.8 38.7 1.0
C A:SER14 4.9 47.2 1.0
CA A:MET17 4.9 41.7 1.0
OG A:SER15 4.9 54.0 1.0
CG A:ARG19 5.0 39.9 1.0

Vanadium binding site 2 out of 4 in 3omx

Go back to Vanadium Binding Sites List in 3omx
Vanadium binding site 2 out of 4 in the Crystal Structure of SSU72 with Vanadate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Crystal Structure of SSU72 with Vanadate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V300

b:50.0
occ:1.00
V B:VO4300 0.0 50.0 1.0
O4 B:VO4300 1.9 45.0 1.0
O3 B:VO4300 1.9 44.9 1.0
O2 B:VO4300 1.9 46.6 1.0
O1 B:VO4300 2.0 60.6 1.0
SG B:CYS13 2.6 43.4 1.0
CB B:CYS13 3.4 44.7 1.0
O B:SER15 3.8 50.8 1.0
N B:ASN18 3.9 43.1 1.0
N B:SER15 4.0 47.7 1.0
NH2 B:ARG19 4.0 45.6 1.0
N B:ARG19 4.0 41.3 1.0
N B:SER14 4.1 49.4 1.0
NE B:ARG19 4.2 43.7 1.0
O B:HOH242 4.2 57.4 1.0
CB B:ASN18 4.3 45.0 1.0
N B:MET17 4.4 45.8 1.0
C B:SER15 4.4 51.3 1.0
CA B:ASN18 4.5 45.1 1.0
OD2 B:ASP144 4.5 57.7 1.0
OD1 B:ASP144 4.5 55.4 1.0
CZ B:ARG19 4.6 44.3 1.0
CB B:SER15 4.6 51.0 1.0
C B:ASN18 4.7 43.6 1.0
CG B:ASP144 4.7 54.0 1.0
CA B:SER15 4.7 48.8 1.0
CA B:CYS13 4.7 43.2 1.0
CB B:MET17 4.8 42.3 1.0
CB B:ARG19 4.8 44.7 1.0
CB B:SER14 4.8 51.2 1.0
C B:CYS13 4.9 48.0 1.0
CA B:SER14 4.9 46.4 1.0
CA B:ARG19 4.9 45.1 1.0
C B:MET17 4.9 45.9 1.0
C B:SER14 5.0 50.5 1.0
CA B:MET17 5.0 47.6 1.0
N B:SER20 5.0 45.0 1.0

Vanadium binding site 3 out of 4 in 3omx

Go back to Vanadium Binding Sites List in 3omx
Vanadium binding site 3 out of 4 in the Crystal Structure of SSU72 with Vanadate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of Crystal Structure of SSU72 with Vanadate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:V300

b:49.3
occ:1.00
V C:VO4300 0.0 49.3 1.0
O4 C:VO4300 1.9 46.3 1.0
O3 C:VO4300 1.9 48.7 1.0
O2 C:VO4300 1.9 50.6 1.0
O1 C:VO4300 2.0 50.1 1.0
SG C:CYS13 2.4 46.5 1.0
CB C:CYS13 3.2 42.7 1.0
N C:ASN18 3.8 47.5 1.0
N C:SER15 3.8 44.5 1.0
N C:ARG19 3.9 45.1 1.0
N C:SER14 4.0 42.9 1.0
N C:ASN16 4.0 45.7 1.0
NE C:ARG19 4.1 42.3 1.0
NH2 C:ARG19 4.1 40.5 1.0
N C:MET17 4.1 47.0 1.0
O C:HOH233 4.4 64.0 1.0
CB C:ASN18 4.4 41.0 1.0
OD1 C:ASP144 4.5 54.4 1.0
CB C:SER15 4.5 46.0 1.0
CA C:ASN18 4.5 46.4 1.0
CA C:SER15 4.5 45.9 1.0
CA C:CYS13 4.6 41.3 1.0
C C:ASN18 4.6 48.6 1.0
C C:SER15 4.6 48.7 1.0
CZ C:ARG19 4.6 44.5 1.0
OD2 C:ASP144 4.7 51.6 1.0
C C:CYS13 4.7 47.0 1.0
CB C:ARG19 4.7 40.0 1.0
CA C:SER14 4.8 47.4 1.0
C C:SER14 4.8 51.5 1.0
CG C:ASP144 4.8 52.0 1.0
OG C:SER20 4.8 45.1 1.0
CA C:ASN16 4.8 46.0 1.0
C C:MET17 4.8 51.2 1.0
CA C:ARG19 4.8 40.2 1.0
CB C:MET17 4.9 43.3 1.0
CA C:MET17 4.9 46.2 1.0
N C:SER20 4.9 40.5 1.0

Vanadium binding site 4 out of 4 in 3omx

Go back to Vanadium Binding Sites List in 3omx
Vanadium binding site 4 out of 4 in the Crystal Structure of SSU72 with Vanadate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 4 of Crystal Structure of SSU72 with Vanadate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:V300

b:69.0
occ:1.00
V D:VO4300 0.0 69.0 1.0
O2 D:VO4300 1.9 59.8 1.0
O3 D:VO4300 1.9 69.5 1.0
O4 D:VO4300 1.9 63.1 1.0
O1 D:VO4300 2.0 63.7 1.0
SG D:CYS13 2.4 61.2 1.0
CB D:CYS13 3.7 59.8 1.0
O D:SER15 3.8 65.2 1.0
N D:ASN18 3.8 59.1 1.0
N D:SER15 3.8 60.6 1.0
NH2 D:ARG19 3.9 63.4 1.0
OD1 D:ASP144 4.0 71.1 1.0
NE D:ARG19 4.0 66.9 1.0
N D:SER14 4.1 63.7 1.0
N D:ARG19 4.2 58.5 1.0
CB D:ASN18 4.2 60.7 1.0
O D:HOH221 4.2 59.2 1.0
C D:SER15 4.4 61.3 1.0
CZ D:ARG19 4.4 72.4 1.0
CB D:SER15 4.4 66.3 1.0
N D:MET17 4.4 57.4 1.0
CA D:ASN18 4.4 56.9 1.0
OD2 D:ASP144 4.5 69.8 1.0
CA D:SER15 4.6 61.7 1.0
CG D:ASP144 4.6 71.5 1.0
O D:HOH215 4.6 70.7 1.0
CB D:MET17 4.7 56.0 1.0
C D:ASN18 4.7 58.4 1.0
C D:SER14 4.8 66.2 1.0
C D:MET17 4.8 58.5 1.0
CA D:SER14 4.8 65.5 1.0
CA D:MET17 4.9 56.3 1.0
CA D:CYS13 4.9 57.8 1.0
CB D:ARG19 4.9 61.6 1.0
C D:CYS13 5.0 59.8 1.0

Reference:

Y.Zhang, M.Zhang, Y.Zhang. Crystal Structure of SSU72, An Essential Eukaryotic Phosphatase Specific For the C-Terminal Domain of Rna Polymerase II, in Complex with A Transition State Analogue. Biochem.J. V. 434 435 2011.
ISSN: ISSN 0264-6021
PubMed: 21204787
DOI: 10.1042/BJ20101471
Page generated: Thu Oct 29 07:05:11 2020

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