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Manganese in PDB 3ori: Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1)

Protein crystallography data

The structure of Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1), PDB code: 3ori was solved by T.N.Lombana, N.Echols, M.C.Good, N.D.Thomsen, H.-L.Ng, T.Alber, Tbstructural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.931, 51.544, 141.409, 90.00, 106.62, 90.00
R / Rfree (%) 20.1 / 25.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1) (pdb code 3ori). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1), PDB code: 3ori:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3ori

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Manganese binding site 1 out of 8 in the Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn341

b:26.5
occ:1.00
 O A:HOH897 1.8 39.5 1.0
O2B A:AGS340 2.2 23.9 1.0
O A:HOH898 2.2 31.9 1.0
OD2 A:ASP156 2.3 20.8 1.0
OD1 A:ASP156 2.3 23.1 1.0
CG A:ASP156 2.6 21.9 1.0
S1G A:AGS340 2.9 35.6 1.0
PB A:AGS340 3.3 23.0 1.0
O3B A:AGS340 3.6 24.7 1.0
PG A:AGS340 3.7 29.3 1.0
MN A:MN342 3.8 42.5 1.0
O A:HOH363 3.8 23.2 1.0
NZ A:LYS40 3.9 20.9 1.0
OE1 A:GLU59 4.0 31.0 1.0
O3G A:AGS340 4.1 28.6 1.0
O1B A:AGS340 4.2 21.4 1.0
CB A:ASP156 4.2 20.6 1.0
OE2 A:GLU59 4.2 31.1 1.0
O A:HOH571 4.4 20.3 1.0
CD A:GLU59 4.5 26.7 1.0
O A:HOH693 4.5 29.7 1.0
NH2 A:ARG55 4.5 32.2 1.0
O3A A:AGS340 4.5 21.9 1.0
O1A A:AGS340 4.6 21.0 1.0
O2A A:AGS340 4.6 25.6 1.0
CE A:LYS40 4.8 23.3 1.0
OD2 A:ASP138 4.8 24.1 1.0
PA A:AGS340 4.8 23.1 1.0

Manganese binding site 2 out of 8 in 3ori

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Manganese binding site 2 out of 8 in the Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn342

b:42.5
occ:1.00
 O2A A:AGS340 2.1 25.6 1.0
OD2 A:ASP156 2.4 20.8 1.0
OD1 A:ASN143 2.4 22.3 1.0
O3G A:AGS340 2.5 28.6 1.0
O3B A:AGS340 2.8 24.7 1.0
PG A:AGS340 3.2 29.3 1.0
CG A:ASP156 3.3 21.9 1.0
PA A:AGS340 3.4 23.1 1.0
CG A:ASN143 3.4 19.2 1.0
O A:HOH592 3.5 19.9 1.0
PB A:AGS340 3.7 23.0 1.0
CB A:ASP156 3.7 20.6 1.0
ND2 A:ASN143 3.7 19.9 1.0
MN A:MN341 3.8 26.5 1.0
O2B A:AGS340 3.8 23.9 1.0
O3A A:AGS340 3.9 21.9 1.0
O1A A:AGS340 4.0 21.0 1.0
CE A:LYS140 4.1 15.7 1.0
S1G A:AGS340 4.1 35.6 1.0
OD1 A:ASP156 4.3 23.1 1.0
NZ A:LYS140 4.3 14.9 1.0
OD2 A:ASP138 4.4 24.1 1.0
O2G A:AGS340 4.5 30.4 1.0
O5' A:AGS340 4.6 27.0 1.0
CB A:ASN143 4.8 17.7 1.0
O A:ALA142 5.0 19.1 1.0

Manganese binding site 3 out of 8 in 3ori

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Manganese binding site 3 out of 8 in the Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn441

b:27.4
occ:1.00
 O B:HOH842 1.5 28.8 1.0
O2B B:AGS440 2.1 24.2 1.0
OD2 B:ASP156 2.3 21.2 1.0
O B:HOH843 2.3 31.8 1.0
O3G B:AGS440 2.4 26.3 1.0
OD1 B:ASP156 2.6 21.5 1.0
CG B:ASP156 2.8 20.7 1.0
PG B:AGS440 3.2 30.0 1.0
PB B:AGS440 3.2 21.6 1.0
O3B B:AGS440 3.4 23.3 1.0
O2G B:AGS440 3.7 26.7 1.0
MN B:MN442 3.8 44.9 1.0
O B:HOH352 4.0 24.1 1.0
O1B B:AGS440 4.2 18.3 1.0
OE1 B:GLU59 4.2 31.1 1.0
NZ B:LYS40 4.2 19.9 1.0
CB B:ASP156 4.3 19.2 1.0
OE2 B:GLU59 4.4 29.0 1.0
O3A B:AGS440 4.5 23.2 1.0
NH2 B:ARG55 4.5 33.6 1.0
O B:HOH403 4.6 19.1 1.0
CD B:GLU59 4.6 26.4 1.0
S1G B:AGS440 4.7 37.5 1.0
O2A B:AGS440 4.7 25.9 1.0
O1A B:AGS440 4.7 25.8 1.0
SD B:MET22 4.8 33.7 1.0
PA B:AGS440 4.8 25.3 1.0
OD2 B:ASP138 4.8 20.1 1.0
CE B:LYS40 5.0 22.1 1.0

Manganese binding site 4 out of 8 in 3ori

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Manganese binding site 4 out of 8 in the Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn442

b:44.9
occ:1.00
 O2A B:AGS440 2.0 25.9 1.0
OD2 B:ASP156 2.4 21.2 1.0
OD1 B:ASN143 2.4 19.6 1.0
O2G B:AGS440 2.5 26.7 1.0
O3B B:AGS440 2.8 23.3 1.0
PG B:AGS440 3.2 30.0 1.0
CG B:ASP156 3.3 20.7 1.0
PA B:AGS440 3.3 25.3 1.0
CG B:ASN143 3.4 17.7 1.0
O B:HOH666 3.6 22.2 1.0
CB B:ASP156 3.6 19.2 1.0
PB B:AGS440 3.7 21.6 1.0
ND2 B:ASN143 3.7 15.8 1.0
O3A B:AGS440 3.7 23.2 1.0
MN B:MN441 3.8 27.4 1.0
O2B B:AGS440 3.9 24.2 1.0
O1A B:AGS440 4.0 25.8 1.0
O3G B:AGS440 4.2 26.3 1.0
CE B:LYS140 4.2 15.3 1.0
OD1 B:ASP156 4.3 21.5 1.0
NZ B:LYS140 4.4 16.9 1.0
O5' B:AGS440 4.5 28.9 1.0
S1G B:AGS440 4.6 37.5 1.0
OD2 B:ASP138 4.7 20.1 1.0
CB B:ASN143 4.8 16.6 1.0
O B:ALA142 4.8 16.3 1.0
O B:HOH842 4.8 28.8 1.0
C5' B:AGS440 5.0 25.0 1.0

Manganese binding site 5 out of 8 in 3ori

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Manganese binding site 5 out of 8 in the Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn541

b:23.8
occ:1.00
 O3G C:AGS540 2.0 16.8 1.0
O2B C:AGS540 2.3 24.3 1.0
OD1 C:ASP156 2.3 20.2 1.0
OD2 C:ASP156 2.4 19.0 1.0
CG C:ASP156 2.7 19.3 1.0
O C:HOH356 2.8 16.5 1.0
OE2 C:GLU59 3.1 37.3 1.0
PG C:AGS540 3.3 25.8 1.0
PB C:AGS540 3.4 22.8 1.0
OE1 C:GLU59 3.5 37.3 1.0
CD C:GLU59 3.6 34.1 1.0
O3B C:AGS540 3.8 22.0 1.0
O C:HOH748 3.9 22.9 1.0
O2G C:AGS540 4.0 25.8 1.0
NZ C:LYS40 4.1 21.3 1.0
MN C:MN542 4.1 25.5 1.0
CB C:ASP156 4.2 18.8 1.0
O C:HOH507 4.2 32.6 1.0
OD2 C:ASP138 4.4 18.5 1.0
O1B C:AGS540 4.4 22.5 1.0
O C:ASP156 4.5 18.0 1.0
O3A C:AGS540 4.6 25.6 1.0
S1G C:AGS540 4.7 28.6 1.0
NH2 C:ARG55 4.7 39.4 1.0
O1A C:AGS540 4.7 25.0 1.0
CE C:MET22 4.7 35.7 1.0
PA C:AGS540 4.9 23.8 1.0
O2A C:AGS540 4.9 24.0 1.0
CG C:GLU59 4.9 31.2 1.0
O C:HOH722 4.9 36.6 1.0
CA C:ASP156 4.9 18.3 1.0

Manganese binding site 6 out of 8 in 3ori

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Manganese binding site 6 out of 8 in the Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn542

b:25.5
occ:1.00
 O2A C:AGS540 2.0 24.0 1.0
O2G C:AGS540 2.0 25.8 1.0
O C:HOH624 2.2 19.1 1.0
OD1 C:ASN143 2.3 18.2 1.0
OD2 C:ASP156 2.3 19.0 1.0
PG C:AGS540 3.0 25.8 1.0
O3B C:AGS540 3.0 22.0 1.0
CG C:ASP156 3.1 19.3 1.0
PA C:AGS540 3.3 23.8 1.0
CG C:ASN143 3.3 17.2 1.0
O3G C:AGS540 3.6 16.8 1.0
CB C:ASP156 3.6 18.8 1.0
ND2 C:ASN143 3.6 19.5 1.0
PB C:AGS540 3.8 22.8 1.0
O3A C:AGS540 3.8 25.6 1.0
O1A C:AGS540 4.0 25.0 1.0
CE C:LYS140 4.1 14.1 1.0
MN C:MN541 4.1 23.8 1.0
O2B C:AGS540 4.1 24.3 1.0
OD1 C:ASP156 4.2 20.2 1.0
NZ C:LYS140 4.2 16.1 1.0
O5' C:AGS540 4.4 24.9 1.0
S1G C:AGS540 4.4 28.6 1.0
O3' C:AGS540 4.6 26.5 1.0
CB C:ASN143 4.6 16.6 1.0
O C:HOH733 4.6 50.6 1.0
OD2 C:ASP138 4.7 18.5 1.0
C5' C:AGS540 4.8 21.3 1.0
O C:ALA142 4.8 18.7 1.0
O C:HOH356 4.9 16.5 1.0
CA C:ASN143 4.9 16.7 1.0

Manganese binding site 7 out of 8 in 3ori

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Manganese binding site 7 out of 8 in the Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn641

b:24.5
occ:1.00
 O3G D:AGS640 2.0 16.3 1.0
OD1 D:ASP156 2.2 19.6 1.0
O2B D:AGS640 2.2 23.0 1.0
OD2 D:ASP156 2.4 21.5 1.0
CG D:ASP156 2.6 21.1 1.0
O D:HOH321 2.9 16.8 1.0
OE1 D:GLU59 3.0 33.7 1.0
PG D:AGS640 3.3 25.2 1.0
PB D:AGS640 3.4 23.1 1.0
O3B D:AGS640 3.7 21.5 1.0
CD D:GLU59 3.9 31.0 1.0
O2G D:AGS640 3.9 26.3 1.0
NZ D:LYS40 3.9 21.5 1.0
O D:HOH668 3.9 27.6 1.0
MN D:MN642 4.1 24.2 1.0
CB D:ASP156 4.1 19.6 1.0
OE2 D:GLU59 4.2 35.1 1.0
O D:HOH563 4.3 42.8 1.0
O1B D:AGS640 4.4 21.4 1.0
OD2 D:ASP138 4.5 21.6 1.0
O D:HOH594 4.5 34.7 1.0
O D:ASP156 4.5 18.9 1.0
O3A D:AGS640 4.5 24.5 1.0
NH2 D:ARG55 4.6 37.9 1.0
O1A D:AGS640 4.6 21.6 1.0
S1G D:AGS640 4.7 25.1 1.0
O2A D:AGS640 4.7 23.6 1.0
PA D:AGS640 4.8 22.1 1.0
CA D:ASP156 4.9 19.1 1.0
CE D:LYS40 5.0 23.1 1.0
C D:ASP156 5.0 19.2 1.0

Manganese binding site 8 out of 8 in 3ori

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Manganese binding site 8 out of 8 in the Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Mycobacterium Tuberculosis Pknb Kinase Domain L33D Mutant (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn642

b:24.2
occ:1.00
 O2A D:AGS640 1.9 23.6 1.0
OD2 D:ASP156 2.1 21.5 1.0
O2G D:AGS640 2.2 26.3 1.0
OD1 D:ASN143 2.2 18.6 1.0
O D:HOH349 2.4 22.4 1.0
O3B D:AGS640 3.0 21.5 1.0
CG D:ASP156 3.1 21.1 1.0
PG D:AGS640 3.1 25.2 1.0
PA D:AGS640 3.2 22.1 1.0
CG D:ASN143 3.3 18.1 1.0
CB D:ASP156 3.5 19.6 1.0
ND2 D:ASN143 3.7 16.8 1.0
O3G D:AGS640 3.7 16.3 1.0
O3A D:AGS640 3.8 24.5 1.0
PB D:AGS640 3.9 23.1 1.0
O1A D:AGS640 4.0 21.6 1.0
O D:HOH630 4.1 32.4 1.0
MN D:MN641 4.1 24.5 1.0
O2B D:AGS640 4.1 23.0 1.0
OD1 D:ASP156 4.1 19.6 1.0
CE D:LYS140 4.2 13.3 1.0
O5' D:AGS640 4.3 22.9 1.0
NZ D:LYS140 4.4 16.5 1.0
O3' D:AGS640 4.5 26.5 1.0
S1G D:AGS640 4.6 25.1 1.0
C5' D:AGS640 4.6 22.3 1.0
CB D:ASN143 4.6 16.8 1.0
O D:ALA142 4.7 17.6 1.0
OD2 D:ASP138 4.7 21.6 1.0
CA D:ASN143 4.9 16.7 1.0
C3' D:AGS640 4.9 24.8 1.0

Reference:

T.N.Lombana, N.Echols, M.C.Good, N.D.Thomsen, H.L.Ng, A.E.Greenstein, A.M.Falick, D.S.King, T.Alber. Allosteric Activation Mechanism of the Mycobacterium Tuberculosis Receptor Ser/Thr Protein Kinase, Pknb. Structure V. 18 1667 2010.
ISSN: ISSN 0969-2126
PubMed: 21134645
DOI: 10.1016/J.STR.2010.09.019
Page generated: Sat Oct 5 17:25:32 2024

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