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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

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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

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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

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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

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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

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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

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