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Sodium in PDB 3mv0: E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One, PDB code: 3mv0 was solved by M.L.Dugdale, M.Vance, M.L.Driedger, A.Nibber, A.Tran, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.23 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.840, 166.310, 201.710, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.7

Other elements in 3mv0:

The structure of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One also contains other interesting chemical elements:

Magnesium (Mg) 11 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One (pdb code 3mv0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One, PDB code: 3mv0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 3mv0

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Sodium binding site 1 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na3101

b:21.9
occ:1.00
 OD1 1:ASN604 2.3 16.8 1.0
O6 1:1492001 2.3 20.0 1.0
O 1:PHE601 2.4 24.6 1.0
O 1:HOH4270 2.4 22.5 1.0
OD2 1:ASP201 2.5 24.2 1.0
CG 1:ASN604 3.2 19.9 1.0
CD2 1:PHE601 3.4 25.0 1.0
CG 1:ASP201 3.4 23.8 1.0
C6 1:1492001 3.4 18.1 1.0
CE2 1:PHE601 3.4 25.3 1.0
ND2 1:ASN604 3.6 19.3 1.0
C 1:PHE601 3.6 24.2 1.0
OD1 1:ASP201 3.8 23.8 1.0
CG 1:PHE601 3.9 26.1 1.0
OH 1:TYR100 4.0 19.1 1.0
O4 1:1492001 4.0 18.0 1.0
CZ 1:PHE601 4.0 26.7 1.0
C4 1:1492001 4.1 19.0 1.0
NE1 1:TRP568 4.1 19.6 1.0
NE2 1:HIS540 4.3 17.8 1.0
C5 1:1492001 4.3 19.1 1.0
CA 1:CYS602 4.4 22.4 1.0
N 1:CYS602 4.5 24.0 1.0
O 1:HOH4050 4.5 23.3 1.0
CD1 1:PHE601 4.5 27.0 1.0
CE1 1:PHE601 4.5 26.4 1.0
CB 1:ASP201 4.6 22.2 1.0
CB 1:ASN604 4.6 18.2 1.0
CA 1:PHE601 4.6 24.4 1.0
CB 1:PHE601 4.6 25.7 1.0
C 1:CYS602 4.8 20.9 1.0
CE1 1:HIS540 4.8 20.0 1.0
O 1:ASP201 4.9 17.4 1.0
CE2 1:TRP568 4.9 21.0 1.0

Sodium binding site 2 out of 16 in 3mv0

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Sodium binding site 2 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na3102

b:29.5
occ:1.00
 O 1:PHE556 2.3 20.1 1.0
O 1:LEU562 2.3 15.6 1.0
O 1:TYR559 2.4 21.3 1.0
O 1:HOH4387 2.7 26.9 1.0
O 1:HOH4557 2.8 54.6 1.0
O 1:PRO560 3.1 15.4 1.0
C 1:TYR559 3.3 17.5 1.0
C 1:LEU562 3.4 15.2 1.0
C 1:PHE556 3.5 17.1 1.0
C 1:PRO560 3.5 16.3 1.0
CA 1:PRO560 3.6 16.1 1.0
O 1:HOH4672 3.7 45.2 1.0
O 1:HOH4277 3.7 21.3 1.0
N 1:PRO560 3.8 17.6 1.0
N 1:LEU562 4.0 13.9 1.0
CA 1:PHE556 4.2 16.9 1.0
CA 1:LEU562 4.2 15.6 1.0
N 1:GLN563 4.3 16.9 1.0
CA 1:GLN563 4.4 15.9 1.0
CA 1:TYR559 4.5 18.3 1.0
CB 1:LEU562 4.5 15.2 1.0
N 1:ARG561 4.5 14.8 1.0
N 1:ARG557 4.5 17.0 1.0
N 1:TYR559 4.5 19.1 1.0
CG 1:GLN563 4.6 17.5 1.0
CA 1:ARG557 4.7 18.1 1.0
C 1:ARG557 4.8 17.5 1.0
CD1 1:LEU350 4.8 22.3 1.0
C 1:ARG561 4.8 16.0 1.0
CB 1:PHE556 4.9 14.5 1.0
O 1:ARG557 5.0 18.7 1.0
O 1:ALA555 5.0 14.4 1.0

Sodium binding site 3 out of 16 in 3mv0

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Sodium binding site 3 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na3103

b:47.3
occ:1.00
 O 1:THR970 2.6 32.7 1.0
O 1:LEU967 2.8 28.6 1.0
O 1:HOH4202 2.8 27.5 1.0
O 1:PRO932 3.0 22.3 1.0
CZ 1:PHE931 3.3 25.5 1.0
O 1:HOH4807 3.6 34.3 1.0
O 1:MET968 3.6 33.6 1.0
CE1 1:PHE931 3.6 25.3 1.0
C 1:THR970 3.7 31.8 1.0
CE2 1:PHE931 3.8 24.1 1.0
C 1:MET968 3.9 33.4 1.0
C 1:LEU967 3.9 27.6 1.0
C 1:PRO932 4.0 23.0 1.0
O 1:HOH4624 4.0 46.3 1.0
CA 1:MET968 4.1 31.6 1.0
N 1:THR970 4.1 31.1 1.0
CD1 1:PHE931 4.3 23.7 1.0
CB 1:PRO932 4.4 24.2 1.0
N 1:MET968 4.4 30.0 1.0
CA 1:THR970 4.5 32.4 1.0
CD2 1:PHE931 4.5 23.2 1.0
CD 1:PRO932 4.5 23.7 1.0
CA 1:PRO932 4.5 23.6 1.0
N 1:SER971 4.6 32.0 1.0
N 1:PRO932 4.6 23.5 1.0
N 1:GLU969 4.6 33.4 1.0
CA 1:SER971 4.7 31.7 1.0
CG 1:PHE931 4.8 23.4 1.0
C 1:GLU969 4.9 32.7 1.0

Sodium binding site 4 out of 16 in 3mv0

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Sodium binding site 4 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Na3104

b:55.4
occ:1.00
 O 1:DMS5018 2.3 68.4 1.0
O 1:LEU670 2.5 33.8 1.0
O 1:SER647 2.5 31.7 1.0
O 1:GLU650 2.7 30.9 1.0
O 1:HOH4720 3.3 54.4 1.0
S 1:DMS5018 3.4 69.3 1.0
N 1:GLU650 3.6 27.7 1.0
C 1:LEU670 3.6 35.0 1.0
C 1:SER647 3.7 31.6 1.0
C 1:GLU650 3.7 30.0 1.0
C1 1:DMS5018 3.9 68.9 1.0
N 1:LEU670 4.0 36.2 1.0
C 1:ASP648 4.0 31.4 1.0
CA 1:ASP648 4.0 30.6 1.0
N 1:ASN649 4.0 30.5 1.0
CA 1:GLU650 4.1 29.1 1.0
CA 1:LEU670 4.2 35.3 1.0
N 1:ASP648 4.3 30.3 1.0
OG 1:SER647 4.4 28.9 1.0
CB 1:LEU670 4.4 35.4 1.0
O 1:ASP648 4.6 31.5 1.0
C 1:ASN649 4.6 28.3 1.0
CB 1:GLU650 4.6 27.8 1.0
CA 1:ASN649 4.7 28.5 1.0
N 1:ASP671 4.7 34.3 1.0
CB 1:SER647 4.8 29.9 1.0
CA 1:SER647 4.9 31.9 1.0
C 1:PRO669 4.9 35.9 1.0
N 1:LEU651 4.9 30.3 1.0
C2 1:DMS5018 4.9 69.1 1.0
CA 1:ASP671 5.0 35.8 1.0

Sodium binding site 5 out of 16 in 3mv0

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Sodium binding site 5 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Na3101

b:18.8
occ:1.00
 OD2 2:ASP201 2.4 19.6 1.0
O 2:PHE601 2.4 19.1 1.0
O 2:HOH4270 2.4 20.3 1.0
O6 2:1492001 2.5 15.1 1.0
OD1 2:ASN604 2.6 19.6 1.0
CD2 2:PHE601 3.3 17.1 1.0
CG 2:ASP201 3.3 20.5 1.0
CE2 2:PHE601 3.4 13.6 1.0
C6 2:1492001 3.5 13.8 1.0
CG 2:ASN604 3.5 20.7 1.0
C 2:PHE601 3.6 20.2 1.0
OD1 2:ASP201 3.8 24.4 1.0
ND2 2:ASN604 3.8 18.0 1.0
CG 2:PHE601 3.9 17.7 1.0
OH 2:TYR100 3.9 19.1 1.0
CZ 2:PHE601 4.0 14.2 1.0
O4 2:1492001 4.0 13.7 1.0
C4 2:1492001 4.1 15.1 1.0
NE1 2:TRP568 4.3 16.7 1.0
CA 2:CYS602 4.3 20.0 1.0
C5 2:1492001 4.4 15.4 1.0
N 2:CYS602 4.4 19.8 1.0
CD1 2:PHE601 4.4 18.3 1.0
CE1 2:PHE601 4.5 18.3 1.0
NE2 2:HIS540 4.5 17.4 1.0
CB 2:ASP201 4.5 16.8 1.0
CB 2:PHE601 4.6 18.4 1.0
CA 2:PHE601 4.6 20.7 1.0
O 2:HOH4052 4.6 10.2 1.0
O 2:ASP201 4.7 18.9 1.0
C 2:CYS602 4.9 18.8 1.0
CB 2:ASN604 4.9 21.2 1.0

Sodium binding site 6 out of 16 in 3mv0

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Sodium binding site 6 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Na3102

b:18.5
occ:1.00
 O 2:TYR559 2.1 17.9 1.0
O 2:PHE556 2.2 16.2 1.0
O 2:LEU562 2.3 15.0 1.0
O 2:HOH4575 2.4 38.4 1.0
O 2:HOH4387 2.9 35.3 1.0
C 2:TYR559 3.1 17.9 1.0
C 2:LEU562 3.3 15.5 1.0
O 2:PRO560 3.4 18.9 1.0
C 2:PHE556 3.4 15.7 1.0
CA 2:PRO560 3.6 17.0 1.0
C 2:PRO560 3.6 17.6 1.0
N 2:PRO560 3.7 17.4 1.0
N 2:LEU562 3.9 15.4 1.0
O 2:HOH4277 3.9 16.5 1.0
CA 2:LEU562 4.1 14.9 1.0
CA 2:PHE556 4.1 15.3 1.0
N 2:GLN563 4.2 15.5 1.0
CA 2:TYR559 4.2 17.2 1.0
CB 2:LEU562 4.3 12.9 1.0
N 2:TYR559 4.4 18.4 1.0
CA 2:GLN563 4.4 15.2 1.0
N 2:ARG557 4.4 16.5 1.0
N 2:ARG561 4.5 16.4 1.0
CG 2:GLN563 4.6 13.8 1.0
CA 2:ARG557 4.6 16.0 1.0
C 2:ARG557 4.7 15.8 1.0
CB 2:PHE556 4.8 17.2 1.0
O 2:ARG557 4.8 17.0 1.0
CD1 2:LEU350 4.8 16.7 1.0
O 2:HOH4902 4.8 53.5 1.0
CB 2:TYR559 4.8 17.5 1.0
C 2:ARG561 4.8 16.7 1.0
O 2:ALA555 4.8 18.5 1.0

Sodium binding site 7 out of 16 in 3mv0

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Sodium binding site 7 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Na3103

b:29.3
occ:1.00
 O 2:PRO932 2.5 22.6 1.0
O 2:LEU967 2.5 25.8 1.0
O 2:THR970 2.6 31.6 1.0
O 2:HOH4204 2.8 22.5 1.0
C 2:PRO932 3.4 22.7 1.0
CZ 2:PHE931 3.6 20.0 1.0
O 2:HOH4651 3.6 49.6 1.0
C 2:THR970 3.7 31.3 1.0
C 2:LEU967 3.7 26.4 1.0
CE2 2:PHE931 3.8 20.3 1.0
CB 2:PRO932 3.8 22.6 1.0
O 2:HOH4510 3.9 27.6 1.0
CE1 2:PHE931 4.0 20.2 1.0
CA 2:PRO932 4.0 23.0 1.0
C 2:MET968 4.1 30.4 1.0
O 2:MET968 4.1 29.4 1.0
N 2:PRO932 4.1 23.8 1.0
CD 2:PRO932 4.2 23.1 1.0
CA 2:MET968 4.2 29.8 1.0
N 2:THR970 4.2 30.8 1.0
CD2 2:PHE931 4.3 21.6 1.0
N 2:MET968 4.4 27.9 1.0
N 2:SER933 4.5 21.6 1.0
CD1 2:PHE931 4.5 23.1 1.0
CA 2:THR970 4.5 31.4 1.0
N 2:SER971 4.6 31.4 1.0
CG 2:PRO932 4.6 22.8 1.0
CA 2:SER971 4.6 30.4 1.0
CG 2:PHE931 4.7 21.3 1.0
N 2:GLU969 4.7 31.3 1.0
C 2:PHE931 4.8 24.2 1.0
CA 2:SER933 4.9 20.0 1.0
CA 2:LEU967 4.9 25.9 1.0

Sodium binding site 8 out of 16 in 3mv0

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Sodium binding site 8 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Na3104

b:34.7
occ:1.00
 O 2:DMS5021 2.5 90.0 1.0
O 2:GLU650 2.6 25.7 1.0
O 2:SER647 2.7 24.6 1.0
O 2:LEU670 2.9 27.1 1.0
C1 2:DMS5021 3.0 89.8 1.0
N 2:GLU650 3.1 24.7 1.0
O 2:HOH4662 3.2 42.4 1.0
S 2:DMS5021 3.4 90.0 1.0
C 2:GLU650 3.5 26.5 1.0
N 2:ASN649 3.5 26.5 1.0
C 2:ASP648 3.6 27.3 1.0
CA 2:GLU650 3.7 24.7 1.0
C 2:SER647 3.7 26.0 1.0
CA 2:ASP648 3.8 27.5 1.0
C 2:LEU670 4.1 29.3 1.0
C 2:ASN649 4.1 24.8 1.0
CA 2:ASN649 4.1 24.9 1.0
O 2:ASP648 4.2 28.5 1.0
N 2:ASP648 4.2 25.9 1.0
CB 2:GLU650 4.2 25.4 1.0
O 2:HOH4704 4.3 42.6 1.0
N 2:LEU670 4.3 31.6 1.0
C2 2:DMS5021 4.7 89.8 1.0
OE1 2:GLU650 4.7 23.0 1.0
CA 2:LEU670 4.7 30.1 1.0
N 2:LEU651 4.7 25.4 1.0
OG 2:SER647 4.7 24.4 1.0
CB 2:LEU670 4.9 30.1 1.0
CA 2:SER647 5.0 25.7 1.0
CB 2:SER647 5.0 25.2 1.0

Sodium binding site 9 out of 16 in 3mv0

Go back to Sodium Binding Sites List in 3mv0
Sodium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Na3101

b:20.3
occ:1.00
 OD1 3:ASN604 2.3 14.7 1.0
O 3:HOH4276 2.4 21.3 1.0
O 3:PHE601 2.4 21.0 1.0
O6 3:1492001 2.4 16.3 1.0
OD2 3:ASP201 2.4 16.9 1.0
CG 3:ASN604 3.3 19.7 1.0
CD2 3:PHE601 3.3 18.2 1.0
CE2 3:PHE601 3.4 18.9 1.0
CG 3:ASP201 3.5 17.0 1.0
C6 3:1492001 3.5 17.0 1.0
C 3:PHE601 3.6 20.1 1.0
ND2 3:ASN604 3.6 18.1 1.0
CG 3:PHE601 3.9 18.2 1.0
OD1 3:ASP201 3.9 19.4 1.0
OH 3:TYR100 4.0 20.7 1.0
O4 3:1492001 4.0 19.6 1.0
CZ 3:PHE601 4.0 15.8 1.0
C4 3:1492001 4.2 21.3 1.0
NE1 3:TRP568 4.3 14.5 1.0
CA 3:CYS602 4.3 19.5 1.0
C5 3:1492001 4.4 19.6 1.0
NE2 3:HIS540 4.4 15.9 1.0
N 3:CYS602 4.4 20.0 1.0
CD1 3:PHE601 4.5 15.7 1.0
CE1 3:PHE601 4.6 16.1 1.0
O 3:HOH4054 4.6 16.3 1.0
CA 3:PHE601 4.6 19.7 1.0
CB 3:PHE601 4.6 18.7 1.0
CB 3:ASP201 4.7 17.1 1.0
CB 3:ASN604 4.7 18.8 1.0
C 3:CYS602 4.8 19.2 1.0
O 3:ASP201 4.9 16.6 1.0
CE1 3:HIS540 4.9 17.7 1.0

Sodium binding site 10 out of 16 in 3mv0

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Sodium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of E. Coli (Lacz) Beta-Galactosidase (R599A) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Na3102

b:24.6
occ:1.00
 O 3:LEU562 2.2 14.4 1.0
O 3:PHE556 2.2 16.3 1.0
O 3:TYR559 2.4 14.8 1.0
O 3:HOH4392 2.8 30.9 1.0
O 3:HOH4565 2.9 37.6 1.0
C 3:LEU562 3.2 14.8 1.0
O 3:PRO560 3.3 17.3 1.0
C 3:TYR559 3.4 16.4 1.0
C 3:PHE556 3.4 16.4 1.0
C 3:PRO560 3.7 15.8 1.0
CA 3:PRO560 3.8 14.4 1.0
O 3:HOH4516 3.8 51.8 1.0
O 3:HOH4283 3.9 28.9 1.0
N 3:LEU562 3.9 14.5 1.0
N 3:PRO560 4.0 13.9 1.0
CA 3:LEU562 4.1 14.5 1.0
N 3:GLN563 4.1 14.6 1.0
CA 3:PHE556 4.1 16.0 1.0
CA 3:GLN563 4.1 15.5 1.0
CB 3:LEU562 4.3 13.7 1.0
N 3:ARG557 4.5 17.2 1.0
CA 3:TYR559 4.5 17.2 1.0
N 3:ARG561 4.6 13.2 1.0
CG 3:GLN563 4.6 16.4 1.0
N 3:TYR559 4.6 18.0 1.0
CA 3:ARG557 4.7 16.8 1.0
CD1 3:LEU350 4.7 19.8 1.0
CB 3:PHE556 4.8 17.1 1.0
C 3:ARG561 4.8 15.4 1.0
C 3:ARG557 4.9 17.3 1.0
O 3:ALA555 4.9 14.7 1.0

Reference:

M.L.Dugdale, M.L.Vance, R.W.Wheatley, M.R.Driedger, A.Nibber, A.Tran, R.E.Huber. Importance of Arg-599 of B-Galactosidase (Escherichia Coli) As An Anchor For the Open Conformations of Phe-601 and the Active-Site Loop Biochem.Cell Biol. V. 88 969 2010.
ISSN: ISSN 0829-8211
Page generated: Mon Oct 7 11:37:34 2024

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