Sodium 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:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Ketoarginine, PDB code: 8rvc:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8rvc

Go back to Sodium Binding Sites List in 8rvc
Sodium 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 Sodium with other atoms in the Na 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:Na1006

b:26.3
occ:1.00
 HD22 A:ASN316 2.1 15.5 0.0
HB3 A:ASN316 2.6 14.7 0.0
O A:LEU312 2.7 17.6 1.0
HD3 A:PRO317 2.9 15.3 0.0
ND2 A:ASN316 3.1 16.7 1.0
HG A:LEU312 3.1 19.3 0.0
HD13 A:LEU312 3.5 19.7 0.0
CB A:ASN316 3.6 16.0 1.0
C A:LEU312 3.7 17.2 1.0
HD21 A:ASN316 3.8 15.7 0.0
CG A:ASN316 3.8 17.7 1.0
HA A:LEU312 3.8 16.1 0.0
HB2 A:ASN316 3.9 14.8 0.0
CD A:PRO317 4.0 16.8 1.0
CG A:LEU312 4.0 20.5 1.0
CD1 A:LEU312 4.2 20.7 1.0
CA A:LEU312 4.3 17.3 1.0
HD12 A:LEU312 4.3 19.8 0.0
HD2 A:PRO317 4.4 15.3 0.0
HA A:ALA313 4.5 15.3 0.0
N A:PRO317 4.7 17.2 1.0
HG3 A:PRO317 4.7 17.2 0.0
CB A:LEU312 4.7 18.2 1.0
CA A:ASN316 4.8 16.1 1.0
N A:ALA313 4.8 16.5 1.0
H A:ASN316 4.9 14.6 0.0
CG A:PRO317 4.9 18.8 1.0
C A:ASN316 5.0 16.4 1.0

Sodium binding site 2 out of 4 in 8rvc

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Sodium 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 Sodium with other atoms in the Na 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:Na1007

b:39.9
occ:1.00
 O A:HOH1220 2.2 38.5 1.0
O A:HOH1202 2.6 50.3 1.0
OD1 A:ASP152 2.6 23.9 1.0
O A:HOH1193 2.7 39.3 1.0
OG1 A:THR154 2.7 22.0 1.0
HB A:THR154 2.9 20.1 0.0
O A:HOH1294 3.0 55.3 1.0
H A:THR154 3.1 18.5 0.0
CB A:THR154 3.4 20.8 1.0
CG A:ASP152 3.4 23.5 1.0
HG1 A:THR154 3.6 21.7 0.0
OD2 A:ASP152 3.8 24.7 1.0
O A:HOH1219 4.0 22.3 1.0
N A:THR154 4.1 19.2 1.0
HA A:ASP152 4.1 18.2 0.0
HG21 A:THR154 4.3 20.5 0.0
CA A:THR154 4.4 19.3 1.0
CG2 A:THR154 4.5 20.9 1.0
HA3 A:GLY217 4.5 22.0 0.0
O A:HOH1289 4.5 42.1 1.0
CB A:ASP152 4.6 19.9 1.0
H A:LYS155 4.6 17.4 0.0
CA A:ASP152 4.6 19.0 1.0
H A:ALA153 4.6 18.1 0.0
C A:ASP152 4.8 19.1 1.0
N A:ALA153 4.8 18.8 1.0
OD1 A:ASP215 4.8 20.6 1.0
OD2 A:ASP215 4.9 22.8 1.0
O A:HOH1112 4.9 31.2 1.0
HG2 A:LYS155 4.9 21.5 0.0
HB2 A:ASP152 4.9 18.9 0.0

Sodium binding site 3 out of 4 in 8rvc

Go back to Sodium Binding Sites List in 8rvc
Sodium 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 Sodium with other atoms in the Na 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
A:Na1008

b:32.6
occ:1.00
 O A:HIS322 2.2 25.1 1.0
O A:GLN327 2.2 25.8 1.0
O A:HOH1263 2.2 41.4 1.0
O A:THR325 2.3 24.6 1.0
H A:GLN327 2.6 25.8 0.0
O A:HOH1258 2.7 39.7 1.0
C A:GLN327 3.4 25.2 1.0
C A:HIS322 3.4 23.9 1.0
HA A:CYS323 3.5 23.6 0.0
N A:GLN327 3.5 25.9 1.0
C A:THR325 3.5 24.8 1.0
HZ3 A:TRP148 3.7 31.7 0.0
HA A:ASN326 3.8 26.5 0.0
H A:THR325 3.8 22.9 0.0
HA A:ASN326 3.8 26.6 0.0
CZ3 A:TRP148 3.9 31.4 1.0
O A:HOH1151 4.0 39.0 1.0
HA A:LEU328 4.0 23.8 0.0
C A:CYS323 4.0 24.0 1.0
CA A:GLN327 4.1 25.3 1.0
CA A:CYS323 4.1 23.8 1.0
HB2 A:GLN327 4.1 26.1 0.0
O A:CYS323 4.2 24.7 1.0
HH2 A:TRP148 4.2 32.5 0.0
CH2 A:TRP148 4.2 31.7 1.0
N A:CYS323 4.2 23.4 1.0
N A:THR325 4.2 23.4 1.0
HA A:HIS322 4.3 22.1 0.0
C A:ASN326 4.4 26.7 1.0
CA A:ASN326 4.4 26.2 0.5
CA A:ASN326 4.4 26.3 0.6
HB3 A:HIS322 4.4 22.5 0.0
N A:ASN326 4.4 25.3 1.0
N A:LEU328 4.5 24.3 1.0
HD13 A:LEU328 4.5 28.0 0.0
HB2 A:LEU328 4.5 24.9 0.0
CA A:HIS322 4.5 22.8 1.0
CA A:THR325 4.5 24.3 1.0
CE3 A:TRP148 4.5 30.4 1.0
N A:PHE324 4.6 22.8 1.0
CA A:LEU328 4.7 23.8 1.0
HD12 A:LEU328 4.7 27.7 0.0
CB A:GLN327 4.7 26.6 1.0
O A:HOH1243 4.7 22.5 1.0
OG1 A:THR325 4.8 27.0 1.0
HE3 A:TRP148 4.8 30.5 0.0
HG1 A:THR325 4.9 26.2 0.0
HA A:GLN327 5.0 25.3 0.0

Sodium binding site 4 out of 4 in 8rvc

Go back to Sodium Binding Sites List in 8rvc
Sodium 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 Sodium with other atoms in the Na 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:Na408

b:32.8
occ:1.00
 O B:GLN327 2.2 29.9 1.0
O B:HIS322 2.3 25.8 1.0
O B:THR325 2.4 25.9 1.0
H B:GLN327 2.6 27.8 0.0
O B:HOH618 2.7 40.3 1.0
C B:GLN327 3.4 29.2 1.0
HA B:CYS323 3.5 24.4 0.0
N B:GLN327 3.5 28.5 1.0
C B:HIS322 3.5 25.2 1.0
C B:THR325 3.6 26.0 1.0
HZ3 B:TRP148 3.7 32.0 0.0
HA B:ASN326 3.8 27.4 0.0
H B:THR325 3.9 22.8 0.0
CZ3 B:TRP148 3.9 32.3 1.0
HA B:LEU328 4.0 28.2 0.0
CA B:GLN327 4.1 28.8 1.0
C B:CYS323 4.1 24.8 1.0
CA B:CYS323 4.1 25.0 1.0
HH2 B:TRP148 4.1 33.0 0.0
CH2 B:TRP148 4.2 32.6 1.0
HB2 B:GLN327 4.2 29.0 0.0
O B:CYS323 4.2 25.1 1.0
N B:CYS323 4.3 25.0 1.0
N B:THR325 4.3 24.1 1.0
HD13 B:LEU328 4.4 33.2 0.0
C B:ASN326 4.4 28.5 1.0
HA B:HIS322 4.4 23.4 0.0
CA B:ASN326 4.4 27.8 0.5
HB2 B:LEU328 4.4 29.7 0.0
CA B:ASN326 4.4 27.7 0.5
N B:LEU328 4.5 28.4 1.0
HB3 B:HIS322 4.5 24.5 0.0
N B:ASN326 4.5 26.7 1.0
CE3 B:TRP148 4.6 31.1 1.0
CA B:HIS322 4.6 24.8 1.0
CA B:THR325 4.6 24.9 1.0
HD12 B:LEU328 4.6 32.9 0.0
CA B:LEU328 4.7 28.3 1.0
N B:PHE324 4.7 23.9 1.0
CB B:GLN327 4.8 30.0 1.0
HE3 B:TRP148 4.8 30.5 0.0
OG1 B:THR325 4.9 26.4 1.0
O B:HOH586 4.9 22.3 1.0
CZ2 B:TRP148 5.0 32.3 1.0
HA B:GLN327 5.0 28.4 0.0

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: Wed Oct 9 13:23:17 2024

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