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Manganese in PDB 6jki: Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa

Enzymatic activity of Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa

All present enzymatic activity of Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa:
2.1.1.228;

Protein crystallography data

The structure of Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa, PDB code: 6jki was solved by J.Jaroensuk, C.W.Liew, S.Atichartpongkul, Y.H.Chionh, Y.H.Wong, W.H.Zhong, M.E.Mcbee, N.Thongdee, E.G.Prestwich, M.S.Demott, S.Mongkolsuk, P.C.Dedon, J.Lescar, M.Fuangthong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.73 / 2.59
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 85.670, 85.670, 147.600, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 25.1

Other elements in 6jki:

The structure of Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa (pdb code 6jki). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa, PDB code: 6jki:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 6jki

Go back to Manganese Binding Sites List in 6jki
Manganese binding site 1 out of 3 in the Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn307

b:0.3
occ:1.00
 N A:SFG306 2.7 78.1 1.0
O B:HOH601 2.9 83.0 1.0
O A:GLU173 2.9 98.4 1.0
OD1 A:ASP174 3.2 98.9 1.0
OD2 A:ASP182 3.2 93.8 1.0
OE1 B:GLU121 3.4 0.2 1.0
O A:SFG306 3.5 79.9 1.0
CA A:ASP174 3.8 94.8 1.0
O B:HOH627 3.8 68.9 1.0
C A:GLU173 3.9 98.9 1.0
CA A:SFG306 3.9 79.0 1.0
CG A:ASP182 3.9 91.2 1.0
CD B:GLU121 4.1 0.3 1.0
C A:SFG306 4.1 83.3 1.0
OE2 B:GLU121 4.2 97.9 1.0
CG A:ASP174 4.2 98.7 1.0
N A:ASP174 4.3 95.7 1.0
OD1 A:ASP182 4.4 94.0 1.0
C3 A:GOL305 4.4 87.5 1.0
C A:ASP174 4.6 95.9 1.0
CB A:ASP174 4.6 96.3 1.0
N A:SER175 4.7 90.8 1.0
CB A:ASP182 4.8 78.0 1.0
CB A:SFG306 4.9 73.6 1.0
OG A:SER175 4.9 98.8 1.0

Manganese binding site 2 out of 3 in 6jki

Go back to Manganese Binding Sites List in 6jki
Manganese binding site 2 out of 3 in the Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn308

b:0.2
occ:1.00
 OE2 A:GLU129 3.5 75.4 1.0
OH B:TYR186 3.5 71.4 1.0
OE1 A:GLU129 3.7 74.7 1.0
O B:ARG196 4.0 80.6 1.0
CD A:GLU129 4.0 85.4 1.0
CZ B:TYR186 4.3 63.1 1.0
CE1 B:TYR186 4.3 52.8 1.0
CG A:ARG126 4.7 59.7 1.0
CD B:PRO198 4.8 73.9 1.0

Manganese binding site 3 out of 3 in 6jki

Go back to Manganese Binding Sites List in 6jki
Manganese binding site 3 out of 3 in the Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn509

b:0.4
occ:1.00
 OD2 B:ASP182 2.3 73.3 1.0
N A:SFG301 2.6 86.1 1.0
O B:GLU173 2.8 94.3 1.0
OE2 A:GLU121 3.0 0.1 1.0
NE2 B:HIS185 3.2 64.5 1.0
CG B:ASP182 3.4 68.3 1.0
CE1 B:HIS185 3.5 63.7 1.0
OD1 B:ASP174 3.6 91.6 1.0
CD A:GLU121 3.6 0.4 1.0
OE2 B:GLU173 3.8 0.1 1.0
CA A:SFG301 3.9 81.7 1.0
OD1 B:ASP182 3.9 66.1 1.0
C B:GLU173 4.0 93.1 1.0
CD B:GLU173 4.1 0.8 1.0
O A:SFG301 4.1 83.5 1.0
OE1 A:GLU121 4.1 0.3 1.0
O A:GLU121 4.1 66.8 1.0
OE1 B:GLU173 4.1 0.4 1.0
C A:SFG301 4.2 83.0 1.0
CB A:GLU121 4.3 64.8 1.0
CD2 B:HIS185 4.4 64.3 1.0
CG A:GLU121 4.5 81.1 1.0
CA B:ASP174 4.5 79.8 1.0
CB B:ASP182 4.6 61.5 1.0
ND1 B:HIS185 4.7 63.6 1.0
CA A:GLU121 4.7 63.4 1.0
CG B:ASP174 4.7 92.5 1.0
CB B:GLU173 4.8 96.6 1.0
N B:ASP174 4.8 82.8 1.0
C A:GLU121 4.9 65.8 1.0
CG B:GLU173 5.0 0.7 1.0

Reference:

J.Jaroensuk, Y.H.Wong, W.Zhong, C.W.Liew, S.Maenpuen, A.E.Sahili, S.Atichartpongkul, Y.H.Chionh, Q.Nah, N.Thongdee, M.E.Mcbee, E.G.Prestwich, M.S.Demott, P.Chaiyen, S.Mongkolsuk, P.C.Dedon, J.Lescar, M.Fuangthong. Crystal Structure and Catalytic Mechanism of the Essential M1G37 Trna Methyltransferase Trmd Frompseudomonas Aeruginosa. Rna V. 25 1481 2019.
ISSN: ESSN 1469-9001
PubMed: 31399541
DOI: 10.1261/RNA.066746.118
Page generated: Sun Oct 6 04:56:58 2024

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