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Magnesium in PDB 3vpb: Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate

Enzymatic activity of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate

All present enzymatic activity of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate:
3.5.1.16;

Protein crystallography data

The structure of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate, PDB code: 3vpb was solved by T.Tomita, T.Ouchi, T.Kuzuyama, M.Nishiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.91 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.546, 113.988, 78.582, 90.00, 102.43, 90.00
R / Rfree (%) 18.7 / 23.5

Other elements in 3vpb:

The structure of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate (pdb code 3vpb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate, PDB code: 3vpb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3vpb

Go back to Magnesium Binding Sites List in 3vpb
Magnesium binding site 1 out of 4 in the Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:16.8
occ:1.00
 O2A A:ADP500 1.9 16.0 1.0
OE2 A:GLU250 2.1 17.3 1.0
OD1 A:ASP237 2.1 22.3 1.0
O4 A:SO4504 2.1 19.7 1.0
O2B A:ADP500 2.1 16.6 1.0
O A:HOH642 2.1 19.0 1.0
CD A:GLU250 3.2 17.8 1.0
PB A:ADP500 3.2 15.9 1.0
PA A:ADP500 3.2 17.6 1.0
CG A:ASP237 3.2 19.3 1.0
S A:SO4504 3.3 20.0 1.0
O3A A:ADP500 3.5 17.6 1.0
ZN A:ZN503 3.6 23.8 1.0
O1B A:ADP500 3.6 18.7 1.0
O2 A:SO4504 3.6 20.7 1.0
CG A:GLU250 3.8 17.3 1.0
OD2 A:ASP237 3.9 22.6 1.0
ND2 A:ASN202 3.9 16.9 1.0
NH2 A:ARG192 4.0 22.6 1.0
C5' A:ADP500 4.1 15.5 1.0
O5' A:ADP500 4.1 15.9 1.0
O A:HOH693 4.2 28.3 1.0
O1 A:SO4504 4.2 20.6 1.0
OE1 A:GLU250 4.2 16.6 1.0
CB A:ASP237 4.3 17.3 1.0
O3' A:ADP500 4.4 18.1 1.0
O3 A:SO4504 4.4 19.5 1.0
O1A A:ADP500 4.4 17.3 1.0
NH1 A:ARG192 4.5 20.7 1.0
O3B A:ADP500 4.5 14.3 1.0
NH2 A:ARG178 4.5 22.2 1.0
C3' A:ADP500 4.7 16.6 1.0
CZ A:ARG192 4.7 20.0 1.0
ND2 A:ASN252 4.7 24.1 1.0
CG A:ASN202 4.8 16.4 1.0
C4' A:ADP500 4.9 16.2 1.0

Magnesium binding site 2 out of 4 in 3vpb

Go back to Magnesium Binding Sites List in 3vpb
Magnesium binding site 2 out of 4 in the Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:17.9
occ:1.00
 O2A B:ADP500 2.0 16.1 1.0
OD2 B:ASP237 2.1 19.6 1.0
OE1 B:GLU250 2.1 18.6 1.0
O3 B:SO4504 2.1 18.1 1.0
O2B B:ADP500 2.1 18.0 1.0
O B:HOH650 2.1 19.4 1.0
PB B:ADP500 3.2 15.6 1.0
CD B:GLU250 3.2 18.8 1.0
CG B:ASP237 3.2 18.5 1.0
PA B:ADP500 3.2 17.7 1.0
S B:SO4504 3.3 19.7 1.0
O3A B:ADP500 3.5 18.4 1.0
O1B B:ADP500 3.5 17.8 1.0
ZN B:ZN503 3.5 23.4 1.0
O1 B:SO4504 3.6 21.0 1.0
CG B:GLU250 3.8 15.9 1.0
OD1 B:ASP237 3.8 21.9 1.0
ND2 B:ASN202 4.0 16.6 1.0
C5' B:ADP500 4.1 15.6 1.0
O5' B:ADP500 4.1 17.4 1.0
O B:HOH727 4.1 32.9 1.0
NH1 B:ARG192 4.2 21.9 1.0
O2 B:SO4504 4.2 19.8 1.0
OE2 B:GLU250 4.2 17.0 1.0
CB B:ASP237 4.3 16.6 1.0
NH2 B:ARG192 4.4 20.4 1.0
O4 B:SO4504 4.4 17.7 1.0
O3' B:ADP500 4.4 17.5 1.0
O1A B:ADP500 4.5 17.9 1.0
O3B B:ADP500 4.5 15.2 1.0
NH2 B:ARG178 4.5 20.4 1.0
ND2 B:ASN252 4.6 19.2 1.0
C3' B:ADP500 4.7 16.6 1.0
CZ B:ARG192 4.7 22.1 1.0
OD1 B:ASN252 4.9 20.2 1.0
CG B:ASN202 4.9 17.0 1.0
C4' B:ADP500 5.0 14.3 1.0

Magnesium binding site 3 out of 4 in 3vpb

Go back to Magnesium Binding Sites List in 3vpb
Magnesium binding site 3 out of 4 in the Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:22.5
occ:1.00
 O C:HOH709 2.0 29.6 1.0
OE1 C:GLU250 2.1 28.3 1.0
O1 C:SO4503 2.2 31.5 1.0
OD2 C:ASP237 2.2 25.3 1.0
O2A C:ADP500 2.2 18.4 1.0
O2B C:ADP500 2.2 22.1 1.0
CD C:GLU250 3.3 27.4 1.0
PB C:ADP500 3.3 20.7 1.0
S C:SO4503 3.3 34.3 1.0
CG C:ASP237 3.4 22.3 1.0
O3 C:SO4503 3.4 35.7 1.0
PA C:ADP500 3.4 19.8 1.0
O1B C:ADP500 3.6 25.1 1.0
O3A C:ADP500 3.7 21.8 1.0
O C:HOH633 3.9 33.3 1.0
CG C:GLU250 3.9 22.4 1.0
ND2 C:ASN202 4.0 20.9 1.0
O C:HOH706 4.1 35.2 1.0
OD1 C:ASP237 4.1 26.9 1.0
NH1 C:ARG192 4.1 27.4 1.0
O4 C:SO4503 4.2 32.6 1.0
C5' C:ADP500 4.2 16.6 1.0
OE2 C:GLU250 4.2 29.6 1.0
O5' C:ADP500 4.3 19.3 1.0
O2 C:SO4503 4.3 35.0 1.0
O3' C:ADP500 4.4 23.2 1.0
CB C:ASP237 4.4 16.8 1.0
NH2 C:ARG192 4.5 29.3 1.0
ND2 C:ASN252 4.5 32.2 1.0
NH2 C:ARG178 4.6 31.1 1.0
O1A C:ADP500 4.7 21.2 1.0
O3B C:ADP500 4.7 23.6 1.0
CZ C:ARG192 4.8 27.3 1.0
C3' C:ADP500 4.8 19.1 1.0
CG C:ASN202 4.9 19.7 1.0

Magnesium binding site 4 out of 4 in 3vpb

Go back to Magnesium Binding Sites List in 3vpb
Magnesium binding site 4 out of 4 in the Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Argx From Sulfolobus Tokodaii Complexed with Lysw/Glu/Adp/Mg/Zn/Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:22.2
occ:1.00
 O D:HOH690 2.1 24.8 1.0
O2 D:SO4503 2.1 36.9 1.0
O2A D:ADP500 2.2 20.2 1.0
O2B D:ADP500 2.2 21.9 1.0
OE2 D:GLU250 2.2 30.2 1.0
OD1 D:ASP237 2.2 28.8 1.0
PB D:ADP500 3.3 21.6 1.0
CD D:GLU250 3.3 27.8 1.0
S D:SO4503 3.3 38.6 1.0
PA D:ADP500 3.4 20.8 1.0
O4 D:SO4503 3.5 39.2 1.0
CG D:ASP237 3.5 22.3 1.0
O1B D:ADP500 3.6 25.8 1.0
O3A D:ADP500 3.7 22.9 1.0
ND2 D:ASN202 3.9 21.9 1.0
O D:HOH654 3.9 34.8 1.0
CG D:GLU250 4.0 23.0 1.0
NH2 D:ARG192 4.0 28.7 1.0
C5' D:ADP500 4.1 19.1 1.0
OD2 D:ASP237 4.2 26.2 1.0
O D:HOH710 4.2 36.4 1.0
O3 D:SO4503 4.2 37.0 1.0
O5' D:ADP500 4.2 20.2 1.0
OE1 D:GLU250 4.3 30.1 1.0
O1 D:SO4503 4.3 37.0 1.0
O3' D:ADP500 4.4 20.6 1.0
CB D:ASP237 4.5 17.2 1.0
NH1 D:ARG192 4.5 26.6 1.0
NH2 D:ARG178 4.5 31.7 1.0
O1A D:ADP500 4.6 21.8 1.0
O3B D:ADP500 4.6 22.1 1.0
C3' D:ADP500 4.7 19.3 1.0
CZ D:ARG192 4.7 27.7 1.0
CG D:ASN202 4.8 21.4 1.0
C4' D:ADP500 5.0 18.6 1.0

Reference:

T.Ouchi, T.Tomita, A.Horie, A.Yoshida, K.Takahashi, H.Nishida, K.Lassak, H.Taka, R.Mineki, T.Fujimura, S.Kosono, C.Nishiyama, R.Masui, S.Kuramitsu, S.V.Albers, T.Kuzuyama, M.Nishiyama. Lysine and Arginine Biosyntheses Mediated By A Common Carrier Protein in Sulfolobus Nat.Chem.Biol. V. 9 277 2013.
ISSN: ISSN 1552-4450
PubMed: 23434852
DOI: 10.1038/NCHEMBIO.1200
Page generated: Thu Aug 15 13:06:21 2024

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