Atomistry » Manganese » PDB 8xia-9xim » 9fz6
Atomistry »
  Manganese »
    PDB 8xia-9xim »
      9fz6 »

Manganese in PDB 9fz6: A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering

Enzymatic activity of A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering

All present enzymatic activity of A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering:
5.6.2.2;

Protein crystallography data

The structure of A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering, PDB code: 9fz6 was solved by H.Morgan, R.Duman, B.D.Bax, A.J.Warren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.72 / 2.58
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 93.633, 93.633, 410.874, 90, 90, 120
R / Rfree (%) 14 / 20

Manganese Binding Sites:

The binding sites of Manganese atom in the A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering (pdb code 9fz6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering, PDB code: 9fz6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 9fz6

Go back to Manganese Binding Sites List in 9fz6
Manganese binding site 1 out of 5 in the A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:50.0
occ:1.00
O B:HOH806 2.1 68.0 1.0
O B:HOH809 2.1 58.7 1.0
OD2 B:ASP510 2.1 45.6 1.0
OD2 B:ASP508 2.2 52.5 1.0
O B:HOH813 2.2 64.7 1.0
O B:HOH810 2.2 45.8 1.0
CG B:ASP510 3.1 50.4 1.0
CG B:ASP508 3.2 63.5 1.0
OD1 B:ASP510 3.4 46.3 1.0
CB B:ASP508 3.5 63.7 1.0
OE2 B:GLU435 4.2 48.2 1.0
OD1 B:ASP508 4.3 61.6 1.0
O G:HOH2207 4.3 40.3 0.7
CB B:ASP510 4.4 52.2 1.0
OP1 E:DG8 4.5 50.1 1.0
CB B:ASP512 4.8 57.5 1.0
CD B:GLU435 4.8 56.5 1.0
OE1 B:GLU435 4.8 51.5 1.0
C5' E:DG8 4.9 56.1 1.0
CA B:ASP508 5.0 66.5 1.0

Manganese binding site 2 out of 5 in 9fz6

Go back to Manganese Binding Sites List in 9fz6
Manganese binding site 2 out of 5 in the A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn901

b:60.9
occ:0.20
O3 C:BTB902 1.9 190.2 0.8
NE2 C:HIS390 2.1 55.4 0.8
N C:BTB902 2.1 58.5 0.2
O4 C:BTB902 2.2 61.3 0.2
NE2 C:HIS390 2.2 62.4 0.2
O3 C:BTB902 2.2 63.3 0.2
O6 C:BTB902 2.2 57.1 0.2
O8 C:BTB902 2.2 57.8 0.2
O4 C:BTB902 2.2 160.0 0.8
CE1 C:HIS390 2.5 62.2 0.8
CE1 C:HIS390 2.5 64.9 0.2
O6 C:BTB902 2.6 177.1 0.8
O8 C:BTB902 2.6 173.9 0.8
C2 C:BTB902 2.7 60.8 0.2
C3 C:BTB902 2.8 60.4 0.2
N C:BTB902 2.8 187.2 0.8
C5 C:BTB902 2.9 57.5 0.2
C6 C:BTB902 2.9 58.0 0.2
C4 C:BTB902 2.9 61.5 0.2
C3 C:BTB902 3.0 185.9 0.8
C7 C:BTB902 3.0 59.8 0.2
C8 C:BTB902 3.1 59.8 0.2
C2 C:BTB902 3.2 184.6 0.8
C4 C:BTB902 3.2 175.1 0.8
CD2 C:HIS390 3.4 59.6 0.8
CD2 C:HIS390 3.5 63.9 0.2
C7 C:BTB902 3.6 187.7 0.8
C8 C:BTB902 3.6 182.4 0.8
C6 C:BTB902 3.7 179.3 0.8
C5 C:BTB902 3.8 182.3 0.8
ND1 C:HIS390 3.8 57.1 0.8
ND1 C:HIS390 3.8 63.9 0.2
C1 C:BTB902 4.2 61.1 0.2
CG C:HIS390 4.3 57.8 0.8
CG C:HIS390 4.3 63.4 0.2
OD2 C:ASP389 4.4 71.4 1.0
CB C:ASP389 4.5 57.3 1.0
C1 C:BTB902 4.7 186.1 0.8
CG C:ASP389 4.9 59.6 1.0

Manganese binding site 3 out of 5 in 9fz6

Go back to Manganese Binding Sites List in 9fz6
Manganese binding site 3 out of 5 in the A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn701

b:59.2
occ:1.00
O D:HOH803 2.2 63.3 1.0
O D:HOH812 2.2 62.2 1.0
O D:HOH809 2.2 57.4 1.0
OD2 D:ASP510 2.2 60.4 1.0
O D:HOH810 2.2 54.7 1.0
OD2 D:ASP508 2.2 69.4 1.0
CG D:ASP510 2.9 66.3 1.0
OD1 D:ASP510 3.1 64.8 1.0
CG D:ASP508 3.2 71.7 1.0
CB D:ASP508 3.5 67.1 1.0
OE2 D:GLU435 4.1 67.3 1.0
CB D:ASP510 4.3 67.8 1.0
OD1 D:ASP508 4.3 69.5 1.0
OP1 F:DG8 4.7 56.7 1.0
CD D:GLU435 5.0 62.9 1.0
CA D:ASP508 5.0 63.4 1.0

Manganese binding site 4 out of 5 in 9fz6

Go back to Manganese Binding Sites List in 9fz6
Manganese binding site 4 out of 5 in the A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn2101

b:89.6
occ:0.60
O G:HOH2206 2.1 70.0 1.0
O G:HOH2201 2.2 67.9 1.0
O G:HOH2203 2.2 78.8 1.0
OP2 G:DG2009 2.2 104.8 0.6
N7 G:DG2009 2.4 98.1 0.6
OG A:SER84 2.4 63.3 1.0
N7 G:DG2009 2.6 94.9 0.4
C8 G:DG2009 2.9 98.0 0.6
C8 G:DG2009 3.0 93.0 0.4
P G:DG2009 3.4 124.4 0.6
OP1 G:DG2009 3.5 88.5 0.4
CB A:SER84 3.6 62.1 1.0
C5 G:DG2009 3.7 100.4 0.6
OP1 G:DG2009 3.9 125.7 0.6
C5 G:DG2009 3.9 95.2 0.4
O5' G:DG2009 4.0 115.9 0.6
O5' G:DG2009 4.2 95.2 0.4
P G:DG2009 4.2 87.1 0.4
N9 G:DG2009 4.2 92.9 0.6
N9 G:DG2009 4.3 88.8 0.4
C7 G:DT2010 4.4 118.6 1.0
O4 G:DT2010 4.5 118.5 1.0
C6 G:DG2009 4.5 101.8 0.6
O6 G:DG2009 4.6 107.6 0.6
C4 G:DG2009 4.6 96.0 0.6
O6 E:DG8 4.6 58.1 1.0
N7 E:DG8 4.7 57.8 1.0
O6 G:DG2009 4.8 101.5 0.4
C6 G:DG2009 4.8 96.1 0.4
C4 G:DG2009 4.8 90.8 0.4
CA A:SER84 5.0 60.5 1.0

Manganese binding site 5 out of 5 in 9fz6

Go back to Manganese Binding Sites List in 9fz6
Manganese binding site 5 out of 5 in the A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of A 2.58A Crystal Structure of S. Aureus Dna Gyrase and Dna with Metals Identified Through Anomalous Scattering within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn2101

b:98.5
occ:0.50
O6 H:DG2009 2.1 99.4 1.0
O G:HOH2202 2.2 96.2 1.0
O H:HOH2204 2.2 101.9 1.0
O C:HOH1100 2.2 99.8 1.0
O H:HOH2208 2.2 96.0 1.0
N4 G:DC2012 2.3 119.7 1.0
C6 H:DG2009 3.2 97.0 1.0
C4 G:DC2012 3.5 122.8 1.0
O6 F:DG8 3.7 77.4 1.0
C5 H:DG2009 4.1 104.5 1.0
N1 H:DG2009 4.1 97.0 1.0
N3 G:DC2012 4.1 125.4 1.0
O G:HOH2205 4.2 61.1 1.0
N4 G:DC2013 4.3 79.6 1.0
N7 H:DG2009 4.3 107.7 1.0
C5 G:DC2012 4.6 125.6 1.0
C6 F:DG8 4.6 65.4 1.0
OG C:SER84 4.8 71.5 1.0

Reference:

H.Morgan, R.Nicholls, A.J.Warren, S.Ward, G.Evans, F.Long, G.Murshudov, R.Duman, B.D.Bax. How Do Gepotidacin and Zolifodacin Stabilize Dna-Cleavage Complexes with Bacterial Type Iia Topoisomerases? 1. Experimental Definition of Metal Binding Sites To Be Published.
Page generated: Thu Oct 31 22:45:36 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy