Magnesium in PDB 8rvc: Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine

Enzymatic activity of Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine

All present enzymatic activity of Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine:
2.1.1.243;

Protein crystallography data

The structure of Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine, PDB code: 8rvc was solved by S.Gerhardt, F.Kemper, J.N.Andexer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.51 / 1.97
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 148.45, 65.873, 75.041, 90, 90, 90
R / Rfree (%) 19.5 / 22

Other elements in 8rvc:

The structure of Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine (pdb code 8rvc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine, PDB code: 8rvc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8rvc

Go back to Magnesium Binding Sites List in 8rvc
Magnesium binding site 1 out of 4 in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:16.1
occ:1.00
 HE2 A:HIS322 1.8 26.6 0.0
O04 A:NWG1001 1.9 39.6 1.0
NE2 A:HIS264 2.0 28.3 1.0
O A:HOH1135 2.1 38.8 1.0
OE1 A:GLN327 2.2 35.3 1.0
O12 A:NWG1001 2.4 39.7 1.0
NE2 A:HIS322 2.7 27.4 1.0
C02 A:NWG1001 2.8 39.7 1.0
CE1 A:HIS264 2.9 28.8 1.0
C01 A:NWG1001 2.9 40.1 1.0
HH A:TYR318 3.0 26.5 0.0
HE1 A:HIS264 3.1 28.1 0.0
CD2 A:HIS264 3.1 26.8 1.0
HE1 A:HIS322 3.2 26.1 0.0
CD A:GLN327 3.3 33.4 1.0
CE1 A:HIS322 3.3 27.3 1.0
HE22 A:GLN327 3.3 32.2 0.0
HD2 A:HIS264 3.4 26.4 0.0
OH A:TYR318 3.6 27.6 1.0
NE2 A:GLN327 3.7 33.1 1.0
CD2 A:HIS322 3.9 26.2 1.0
O03 A:NWG1001 4.0 39.7 1.0
HG2 A:GLU265 4.0 32.6 0.0
HB3 A:PHE261 4.0 21.1 0.0
ND1 A:HIS264 4.1 28.2 1.0
HG3 A:GLU265 4.1 32.6 0.0
CG A:HIS264 4.1 25.8 1.0
HB3 A:GLN327 4.2 26.1 0.0
HE1 A:TYR318 4.2 22.9 0.0
HD2 A:HIS322 4.3 25.6 0.0
HD21 A:LEU329 4.3 21.7 0.0
CZ A:TYR318 4.3 25.1 1.0
OE2 A:GLU265 4.4 44.6 1.0
C05 A:NWG1001 4.4 40.6 1.0
HH12 A:ARG151 4.4 31.8 0.0
CG A:GLU265 4.5 33.0 1.0
ND1 A:HIS322 4.5 26.3 1.0
HH A:TYR131 4.5 20.4 0.0
CE1 A:TYR318 4.6 24.2 1.0
CG A:GLN327 4.6 29.6 1.0
O A:PHE261 4.6 23.6 1.0
HE21 A:GLN327 4.7 32.3 0.0
H1 A:NWG1001 4.7 39.5 0.0
HG2 A:GLN327 4.8 29.3 0.0
CG A:HIS322 4.8 24.7 1.0
H3 A:NWG1001 4.8 40.6 0.0
H10 A:NWG1001 4.9 41.4 0.0
CB A:GLN327 4.9 26.6 1.0
HD11 A:LEU321 4.9 23.4 0.0
OH A:TYR131 4.9 21.6 1.0
HD1 A:HIS264 4.9 27.8 0.0
CD A:GLU265 5.0 42.4 1.0

Magnesium binding site 2 out of 4 in 8rvc

Go back to Magnesium Binding Sites List in 8rvc
Magnesium binding site 2 out of 4 in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1009

b:42.6
occ:1.00
 O A:GLY260 2.4 21.6 1.0
O A:HOH1196 2.5 36.7 1.0
O A:GLY190 2.6 26.0 1.0
O A:HOH1101 2.6 27.8 1.0
O A:HOH1223 2.9 65.3 1.0
HA3 A:GLY260 3.3 21.0 0.0
HG23 A:VAL262 3.4 25.5 0.0
C A:GLY260 3.4 21.5 1.0
H A:GLY260 3.5 21.0 0.0
CA A:GLY260 3.7 21.4 1.0
C A:GLY190 3.7 25.7 1.0
N A:GLY260 4.0 21.1 1.0
HD2 A:PHE261 4.0 23.2 0.0
HA3 A:GLY190 4.0 26.3 0.0
HG22 A:VAL262 4.0 25.5 0.0
CG2 A:VAL262 4.1 25.7 1.0
O A:HOH1261 4.1 41.5 1.0
HA A:CYS191 4.1 24.1 0.0
O A:HOH1271 4.1 53.5 1.0
O A:LEU189 4.1 28.3 1.0
HG21 A:VAL262 4.2 25.8 0.0
HB2 A:PHE261 4.3 21.1 0.0
HH A:TYR196 4.3 36.2 0.0
OD1 A:ASP188 4.4 30.1 1.0
CA A:GLY190 4.5 26.3 1.0
OH A:TYR196 4.5 36.9 1.0
HE1 A:TYR196 4.5 34.0 0.0
N A:PHE261 4.6 21.2 1.0
CE1 A:TYR196 4.6 34.6 1.0
CZ A:TYR196 4.6 35.5 1.0
N A:CYS191 4.7 24.6 1.0
HA2 A:GLY260 4.7 21.1 0.0
CA A:CYS191 4.8 24.2 1.0
CD2 A:PHE261 5.0 24.0 1.0
HG12 A:VAL258 5.0 23.8 0.0

Magnesium binding site 3 out of 4 in 8rvc

Go back to Magnesium Binding Sites List in 8rvc
Magnesium binding site 3 out of 4 in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:24.6
occ:1.00
 HE2 B:HIS322 1.8 28.9 0.0
O04 B:NWG407 1.9 45.4 1.0
NE2 B:HIS264 2.0 34.3 1.0
OE1 B:GLN327 2.2 38.2 1.0
O B:HOH522 2.3 48.7 1.0
O12 B:NWG407 2.4 45.7 1.0
NE2 B:HIS322 2.7 30.2 1.0
C02 B:NWG407 2.8 45.5 1.0
CE1 B:HIS264 2.9 34.9 1.0
C01 B:NWG407 2.9 45.8 1.0
HH B:TYR318 3.0 26.3 0.0
HE1 B:HIS264 3.1 34.0 0.0
CD2 B:HIS264 3.1 33.1 1.0
HE1 B:HIS322 3.2 28.6 0.0
CD B:GLN327 3.3 36.5 1.0
CE1 B:HIS322 3.3 30.3 1.0
HE22 B:GLN327 3.3 34.8 0.0
HD2 B:HIS264 3.4 32.4 0.0
OH B:TYR318 3.6 27.7 1.0
NE2 B:GLN327 3.7 36.5 1.0
CD2 B:HIS322 3.9 28.8 1.0
HG2 B:GLU265 4.0 35.8 0.0
O03 B:NWG407 4.0 45.6 1.0
HB3 B:PHE261 4.0 23.8 0.0
ND1 B:HIS264 4.1 34.3 1.0
HG3 B:GLU265 4.1 36.0 0.0
CG B:HIS264 4.1 31.9 1.0
HB3 B:GLN327 4.2 29.1 0.0
HE1 B:TYR318 4.2 24.2 0.0
HD2 B:HIS322 4.3 27.8 0.0
HD21 B:LEU329 4.3 24.6 0.0
CZ B:TYR318 4.3 26.8 1.0
OE2 B:GLU265 4.4 48.6 1.0
C05 B:NWG407 4.4 46.1 1.0
HH12 B:ARG151 4.4 34.0 0.0
CG B:GLU265 4.5 36.7 1.0
ND1 B:HIS322 4.5 29.6 1.0
CG B:GLN327 4.5 32.4 1.0
HH B:TYR131 4.6 22.1 0.0
CE1 B:TYR318 4.6 26.0 1.0
O B:PHE261 4.6 26.9 1.0
HE21 B:GLN327 4.7 34.9 0.0
H1 B:NWG407 4.7 44.5 0.0
HG2 B:GLN327 4.8 31.4 0.0
CG B:HIS322 4.8 27.5 1.0
H3 B:NWG407 4.8 45.5 0.0
CB B:GLN327 4.9 30.0 1.0
H10 B:NWG407 4.9 45.9 0.0
HD11 B:LEU321 4.9 23.7 0.0
OH B:TYR131 4.9 24.1 1.0
HD1 B:HIS264 5.0 33.9 0.0
CD B:GLU265 5.0 45.9 1.0

Magnesium binding site 4 out of 4 in 8rvc

Go back to Magnesium Binding Sites List in 8rvc
Magnesium binding site 4 out of 4 in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg409

b:42.4
occ:1.00
 O B:HOH627 2.2 39.5 1.0
O B:HOH503 2.3 30.9 1.0
O B:GLY260 2.4 25.2 1.0
O B:GLY190 2.5 32.4 1.0
O B:HOH573 2.5 38.5 1.0
HG23 B:VAL262 3.1 29.1 0.0
H B:GLY260 3.2 26.5 0.0
HA3 B:GLY260 3.3 26.0 0.0
C B:GLY260 3.4 25.4 1.0
C B:GLY190 3.5 32.3 1.0
CA B:GLY260 3.7 25.9 1.0
O B:LEU189 3.7 34.8 1.0
HA3 B:GLY190 3.8 32.9 0.0
CG2 B:VAL262 3.8 29.1 1.0
HG22 B:VAL262 3.8 28.9 0.0
N B:GLY260 3.8 26.0 1.0
HG21 B:VAL262 3.8 29.4 0.0
HA B:CYS191 4.0 31.3 0.0
OD1 B:ASP188 4.2 40.5 1.0
CA B:GLY190 4.2 33.0 1.0
HD2 B:PHE261 4.3 25.4 0.0
HB2 B:PHE261 4.5 23.9 0.0
N B:CYS191 4.5 31.4 1.0
N B:PHE261 4.6 24.9 1.0
C B:LEU189 4.7 34.1 1.0
CA B:CYS191 4.7 31.2 1.0
HA2 B:GLY260 4.7 26.2 0.0
HG12 B:VAL258 4.8 31.9 0.0
OH B:TYR196 4.8 43.3 1.0
CZ B:TYR196 4.9 42.1 1.0
HH B:TYR196 4.9 42.8 0.0
N B:GLY190 4.9 33.4 1.0
HA B:LEU259 4.9 27.9 0.0
CE2 B:TYR196 5.0 41.2 1.0
HE2 B:TYR196 5.0 40.9 0.0
C B:LEU259 5.0 26.7 1.0

Reference:

C.Sommer-Kamann, J.Breiltgens, Z.Zou, S.Gerhardt, R.Saleem-Batcha, F.Kemper, O.Einsle, J.N.Andexer, M.Muller. Structures and Protein Engineering of the Alpha-Keto Acid C-Methyltransferases Sgvm and Mrsa For Rational Substrate Transfer. Chembiochem 00258 2024.
ISSN: ESSN 1439-7633
PubMed: 38887142
DOI: 10.1002/CBIC.202400258
Page generated: Fri Oct 4 17:54:33 2024

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