Magnesium in PDB 7waf: Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg)

Enzymatic activity of Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg)

All present enzymatic activity of Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg):
6.3.2.29; 6.3.2.30;

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg) (pdb code 7waf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg), PDB code: 7waf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 7waf

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Magnesium binding site 1 out of 12 in the Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:67.9
occ:1.00
 OE2 A:GLU450 2.2 61.7 1.0
OE1 A:GLU450 2.2 61.7 1.0
CD A:GLU450 2.5 61.7 1.0
O2G A:AGS1004 2.6 89.2 1.0
OD1 A:ASN452 2.8 53.7 1.0
O2B A:AGS1004 3.5 89.2 1.0
MG A:MG1002 3.9 74.5 1.0
CG A:ASN452 4.0 53.7 1.0
PG A:AGS1004 4.0 89.2 1.0
CG A:GLU450 4.1 61.7 1.0
O1A A:AGS1004 4.1 89.2 1.0
CE A:LYS220 4.2 66.3 1.0
O3G A:AGS1004 4.4 89.2 1.0
NZ A:LYS220 4.4 66.3 1.0
ND2 A:ASN452 4.6 53.7 1.0
PB A:AGS1004 4.8 89.2 1.0
CB A:GLU450 4.8 61.7 1.0
O3B A:AGS1004 5.0 89.2 1.0

Magnesium binding site 2 out of 12 in 7waf

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Magnesium binding site 2 out of 12 in the Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:74.5
occ:1.00
 OD2 A:ASP431 2.1 58.3 1.0
OE2 A:GLU450 2.2 61.7 1.0
O1A A:AGS1004 3.1 89.2 1.0
CD A:GLU450 3.2 61.7 1.0
CG A:ASP431 3.2 58.3 1.0
O2G A:AGS1004 3.4 89.2 1.0
CG A:GLU450 3.7 61.7 1.0
S1G A:AGS1004 3.9 89.2 1.0
MG A:MG1001 3.9 67.9 1.0
OD1 A:ASP431 4.0 58.3 1.0
O3' A:AGS1004 4.2 89.2 1.0
CB A:ASP431 4.2 58.3 1.0
NH1 A:ARG323 4.2 76.1 1.0
OE1 A:GLU450 4.3 61.7 1.0
PG A:AGS1004 4.3 89.2 1.0
NH2 A:ARG309 4.3 55.6 1.0
ND2 A:ASN452 4.4 53.7 1.0
PA A:AGS1004 4.5 89.2 1.0
OD1 A:ASN452 4.5 53.7 1.0
C5' A:AGS1004 4.8 89.2 1.0
O2B A:AGS1004 4.9 89.2 1.0
CG A:ASN452 4.9 53.7 1.0
O5' A:AGS1004 4.9 89.2 1.0
C3' A:AGS1004 5.0 89.2 1.0

Magnesium binding site 3 out of 12 in 7waf

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Magnesium binding site 3 out of 12 in the Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:71.0
occ:1.00
 OG1 A:THR500 2.0 63.6 1.0
O2B A:AGS1005 2.0 79.3 1.0
O3G A:AGS1005 2.0 79.3 1.0
OG1 A:THR522 2.0 66.9 1.0
OE2 A:GLU558 2.6 57.3 1.0
PB A:AGS1005 2.9 79.3 1.0
O3A A:AGS1005 3.0 79.3 1.0
CB A:THR522 3.0 66.9 1.0
PG A:AGS1005 3.3 79.3 1.0
NH2 A:ARG731 3.3 101.5 1.0
CB A:THR500 3.3 63.6 1.0
O3B A:AGS1005 3.5 79.3 1.0
CD A:GLU558 3.5 57.3 1.0
OE1 A:GLU558 3.6 57.3 1.0
CG2 A:THR522 3.8 66.9 1.0
N A:THR500 4.0 63.6 1.0
CA A:THR500 4.2 63.6 1.0
O2G A:AGS1005 4.2 79.3 1.0
CA A:THR522 4.3 66.9 1.0
O1B A:AGS1005 4.3 79.3 1.0
CG2 A:THR500 4.3 63.6 1.0
N A:THR522 4.3 66.9 1.0
CZ A:ARG731 4.5 101.5 1.0
PA A:AGS1005 4.5 79.3 1.0
S1G A:AGS1005 4.7 79.3 1.0
CE2 A:TYR746 4.7 110.5 1.0
CG A:GLU558 4.9 57.3 1.0
CB A:LYS499 4.9 60.0 1.0
NE A:ARG731 4.9 101.5 1.0
CE A:LYS499 5.0 60.0 1.0

Magnesium binding site 4 out of 12 in 7waf

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Magnesium binding site 4 out of 12 in the Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:68.6
occ:1.00
 OE2 B:GLU450 2.2 62.0 1.0
OE1 B:GLU450 2.2 62.0 1.0
CD B:GLU450 2.5 62.0 1.0
O2G B:AGS1004 2.5 89.9 1.0
OD1 B:ASN452 2.9 54.4 1.0
O2B B:AGS1004 3.5 89.9 1.0
MG B:MG1002 3.8 75.7 1.0
PG B:AGS1004 4.0 89.9 1.0
CG B:ASN452 4.0 54.4 1.0
CG B:GLU450 4.1 62.0 1.0
O1A B:AGS1004 4.1 89.9 1.0
CE B:LYS220 4.2 66.7 1.0
O3G B:AGS1004 4.4 89.9 1.0
NZ B:LYS220 4.4 66.7 1.0
ND2 B:ASN452 4.6 54.4 1.0
PB B:AGS1004 4.8 89.9 1.0
CB B:GLU450 4.9 62.0 1.0
O3B B:AGS1004 5.0 89.9 1.0

Magnesium binding site 5 out of 12 in 7waf

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Magnesium binding site 5 out of 12 in the Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:75.7
occ:1.00
 OD2 B:ASP431 2.1 58.5 1.0
OE2 B:GLU450 2.2 62.0 1.0
O1A B:AGS1004 3.1 89.9 1.0
CD B:GLU450 3.2 62.0 1.0
CG B:ASP431 3.2 58.5 1.0
O2G B:AGS1004 3.4 89.9 1.0
CG B:GLU450 3.7 62.0 1.0
MG B:MG1001 3.8 68.6 1.0
S1G B:AGS1004 3.9 89.9 1.0
OD1 B:ASP431 4.0 58.5 1.0
CB B:ASP431 4.2 58.5 1.0
O3' B:AGS1004 4.2 89.9 1.0
NH1 B:ARG323 4.2 75.5 1.0
OE1 B:GLU450 4.3 62.0 1.0
PG B:AGS1004 4.3 89.9 1.0
NH2 B:ARG309 4.3 55.4 1.0
ND2 B:ASN452 4.4 54.4 1.0
PA B:AGS1004 4.5 89.9 1.0
OD1 B:ASN452 4.5 54.4 1.0
C5' B:AGS1004 4.8 89.9 1.0
O2B B:AGS1004 4.9 89.9 1.0
CG B:ASN452 4.9 54.4 1.0
O5' B:AGS1004 4.9 89.9 1.0
C3' B:AGS1004 5.0 89.9 1.0

Magnesium binding site 6 out of 12 in 7waf

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Magnesium binding site 6 out of 12 in the Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:71.7
occ:1.00
 O2B B:AGS1005 2.0 79.1 1.0
OG1 B:THR500 2.0 63.7 1.0
O3G B:AGS1005 2.0 79.1 1.0
OG1 B:THR522 2.0 66.9 1.0
OE2 B:GLU558 2.6 57.2 1.0
PB B:AGS1005 3.0 79.1 1.0
O3A B:AGS1005 3.0 79.1 1.0
CB B:THR522 3.0 66.9 1.0
NH2 B:ARG731 3.3 101.5 1.0
PG B:AGS1005 3.3 79.1 1.0
CB B:THR500 3.3 63.7 1.0
O3B B:AGS1005 3.5 79.1 1.0
CD B:GLU558 3.5 57.2 1.0
OE1 B:GLU558 3.6 57.2 1.0
CG2 B:THR522 3.8 66.9 1.0
N B:THR500 4.0 63.7 1.0
CA B:THR500 4.2 63.7 1.0
O2G B:AGS1005 4.2 79.1 1.0
CA B:THR522 4.3 66.9 1.0
O1B B:AGS1005 4.3 79.1 1.0
CG2 B:THR500 4.3 63.7 1.0
N B:THR522 4.3 66.9 1.0
CZ B:ARG731 4.5 101.5 1.0
PA B:AGS1005 4.5 79.1 1.0
CE2 B:TYR746 4.6 109.8 1.0
S1G B:AGS1005 4.6 79.1 1.0
CG B:GLU558 4.9 57.2 1.0
CB B:LYS499 4.9 59.9 1.0
NE B:ARG731 4.9 101.5 1.0
CE B:LYS499 5.0 59.9 1.0
CD2 B:TYR746 5.0 109.8 1.0
O2A B:AGS1005 5.0 79.1 1.0

Magnesium binding site 7 out of 12 in 7waf

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Magnesium binding site 7 out of 12 in the Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:74.3
occ:1.00
 OD1 C:ASN266 2.4 101.8 1.0
OE2 C:GLU450 2.6 61.3 1.0
OD1 C:ASN452 2.7 55.2 1.0
OE1 C:GLU450 2.8 61.3 1.0
O2G C:AGS1004 2.8 86.9 1.0
CD C:GLU450 3.1 61.3 1.0
O3G C:AGS1004 3.1 86.9 1.0
O2B C:AGS1004 3.2 86.9 1.0
CG C:ASN266 3.4 101.8 1.0
PG C:AGS1004 3.6 86.9 1.0
CG C:ASN452 3.8 55.2 1.0
ND2 C:ASN266 3.9 101.8 1.0
MG C:MG1002 4.1 74.0 1.0
ND2 C:ASN452 4.4 55.2 1.0
PB C:AGS1004 4.4 86.9 1.0
O3B C:AGS1004 4.4 86.9 1.0
CB C:ASN266 4.5 101.8 1.0
CG C:GLU450 4.6 61.3 1.0
CA C:ASN266 4.6 101.8 1.0
O1A C:AGS1004 4.7 86.9 1.0
CE C:LYS220 4.7 65.1 1.0
NZ C:LYS220 4.7 65.1 1.0
N C:HIS267 4.8 101.6 1.0
CB C:ASN452 5.0 55.2 1.0

Magnesium binding site 8 out of 12 in 7waf

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Magnesium binding site 8 out of 12 in the Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:74.0
occ:1.00
 OD2 C:ASP431 2.1 58.2 1.0
O3G C:AGS1004 2.1 86.9 1.0
OE2 C:GLU450 2.3 61.3 1.0
PG C:AGS1004 3.1 86.9 1.0
CG C:ASP431 3.1 58.2 1.0
S1G C:AGS1004 3.2 86.9 1.0
O1A C:AGS1004 3.3 86.9 1.0
CD C:GLU450 3.4 61.3 1.0
NH2 C:ARG323 3.6 72.1 1.0
OD1 C:ASP431 3.7 58.2 1.0
O2G C:AGS1004 3.9 86.9 1.0
CG C:GLU450 3.9 61.3 1.0
MG C:MG1001 4.1 74.3 1.0
CB C:ASP431 4.2 58.2 1.0
ND2 C:ASN452 4.2 55.2 1.0
NH2 C:ARG309 4.2 55.6 1.0
O3' C:AGS1004 4.3 86.9 1.0
O2B C:AGS1004 4.3 86.9 1.0
O3B C:AGS1004 4.4 86.9 1.0
OE1 C:GLU450 4.4 61.3 1.0
CZ C:ARG323 4.6 72.1 1.0
OD1 C:ASN452 4.6 55.2 1.0
PA C:AGS1004 4.7 86.9 1.0
NH1 C:ARG323 4.8 72.1 1.0
CG C:ASN452 4.8 55.2 1.0
PB C:AGS1004 5.0 86.9 1.0

Magnesium binding site 9 out of 12 in 7waf

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Magnesium binding site 9 out of 12 in the Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:59.8
occ:1.00
 O2B C:AGS1005 2.0 63.4 1.0
OG1 C:THR522 2.0 62.1 1.0
OG1 C:THR500 2.1 54.5 1.0
O3G C:AGS1005 2.1 63.4 1.0
CB C:THR522 2.9 62.1 1.0
OE2 C:GLU558 3.0 54.7 1.0
PG C:AGS1005 3.1 63.4 1.0
PB C:AGS1005 3.1 63.4 1.0
O3A C:AGS1005 3.3 63.4 1.0
CB C:THR500 3.3 54.5 1.0
O3B C:AGS1005 3.5 63.4 1.0
S1G C:AGS1005 3.5 63.4 1.0
CG2 C:THR522 3.6 62.1 1.0
CD C:GLU558 3.8 54.7 1.0
OE1 C:GLU558 3.8 54.7 1.0
CA C:THR522 4.2 62.1 1.0
CG2 C:THR500 4.2 54.5 1.0
N C:THR522 4.3 62.1 1.0
N C:THR500 4.3 54.5 1.0
CA C:THR500 4.3 54.5 1.0
O1B C:AGS1005 4.4 63.4 1.0
O2G C:AGS1005 4.5 63.4 1.0
PA C:AGS1005 4.6 63.4 1.0
O2A C:AGS1005 4.8 63.4 1.0
O1A C:AGS1005 4.9 63.4 1.0

Magnesium binding site 10 out of 12 in 7waf

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Magnesium binding site 10 out of 12 in the Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Trichodesmium Erythraeum Cyanophycin Synthetase 1 (TECPHA1) with Atpgammas and 4X(Beta-Asp-Arg) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1001

b:73.8
occ:1.00
 OD1 D:ASN266 2.3 101.8 1.0
OE2 D:GLU450 2.6 61.1 1.0
OD1 D:ASN452 2.7 54.2 1.0
O2G D:AGS1004 2.8 87.0 1.0
OE1 D:GLU450 2.8 61.1 1.0
CD D:GLU450 3.1 61.1 1.0
O3G D:AGS1004 3.1 87.0 1.0
O2B D:AGS1004 3.2 87.0 1.0
CG D:ASN266 3.3 101.8 1.0
PG D:AGS1004 3.5 87.0 1.0
CG D:ASN452 3.9 54.2 1.0
ND2 D:ASN266 3.9 101.8 1.0
MG D:MG1002 4.0 73.9 1.0
OXT K:ARG102 4.3 86.5 1.0
PB D:AGS1004 4.4 87.0 1.0
O3B D:AGS1004 4.4 87.0 1.0
ND2 D:ASN452 4.4 54.2 1.0
CB D:ASN266 4.5 101.8 1.0
CG D:GLU450 4.6 61.1 1.0
CA D:ASN266 4.6 101.8 1.0
O1A D:AGS1004 4.6 87.0 1.0
NZ D:LYS220 4.7 65.2 1.0
CE D:LYS220 4.7 65.2 1.0
N D:HIS267 4.7 101.4 1.0

Reference:

T.Miyakawa, J.Yang, M.Kawasaki, N.Adachi, A.Fujii, Y.Miyauchi, T.Muramatsu, T.Moriya, T.Senda, M.Tanokura. Structural Bases For Aspartate Recognition and Polymerization Efficiency of Cyanobacterial Cyanophycin Synthetase. Nat Commun V. 13 5097 2022.
ISSN: ESSN 2041-1723
PubMed: 36042318
DOI: 10.1038/S41467-022-32834-8
Page generated: Thu Oct 3 11:13:45 2024

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