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Gadolinium in PDB 8rt2: Hen Egg White Lysozyme Crystallized with Bioassembler on Earth

Enzymatic activity of Hen Egg White Lysozyme Crystallized with Bioassembler on Earth

All present enzymatic activity of Hen Egg White Lysozyme Crystallized with Bioassembler on Earth:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg White Lysozyme Crystallized with Bioassembler on Earth, PDB code: 8rt2 was solved by C.Maccarthy, E.V.Koudan, S.V.Petrov, A.A.Levin, Y.D.Khesuani, V.Borshchevskiy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.73 / 0.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.03, 77.03, 38.97, 90, 90, 90
R / Rfree (%) 12.1 / 13.3

Other elements in 8rt2:

The structure of Hen Egg White Lysozyme Crystallized with Bioassembler on Earth also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 7 atoms

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Hen Egg White Lysozyme Crystallized with Bioassembler on Earth (pdb code 8rt2). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 4 binding sites of Gadolinium where determined in the Hen Egg White Lysozyme Crystallized with Bioassembler on Earth, PDB code: 8rt2:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 8rt2

Go back to Gadolinium Binding Sites List in 8rt2
Gadolinium binding site 1 out of 4 in the Hen Egg White Lysozyme Crystallized with Bioassembler on Earth


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Hen Egg White Lysozyme Crystallized with Bioassembler on Earth within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1001

b:10.0
occ:0.76
GD A:GD1001 0.0 10.0 0.8
GD A:GD1001 1.3 14.7 0.2
HO7 A:DO31002 2.0 14.4 0.8
O7 A:DO31002 2.3 12.5 0.8
O5 A:DO31002 2.3 12.7 0.8
O1 A:DO31002 2.4 11.7 0.8
O3 A:DO31002 2.4 10.7 0.8
O A:HOH1127 2.5 12.4 0.8
N1 A:DO31002 2.6 11.7 0.8
N4 A:DO31002 2.6 13.7 0.8
N3 A:DO31002 2.6 13.0 0.8
N2 A:DO31002 2.7 11.4 0.8
C13 A:DO31002 3.1 14.2 0.8
C10 A:DO31002 3.2 12.7 0.8
C9 A:DO31002 3.2 11.6 0.8
H101 A:DO31002 3.2 15.7 0.8
C11 A:DO31002 3.2 12.3 0.8
C14 A:DO31002 3.2 13.7 0.8
C12 A:DO31002 3.3 12.2 0.8
C16 A:DO31002 3.3 13.8 0.8
C15 A:DO31002 3.4 14.6 0.8
H161 A:DO31002 3.4 15.2 0.8
H142 A:DO31002 3.4 14.6 0.8
H122 A:DO31002 3.5 13.6 0.8
C8 A:DO31002 3.5 13.5 0.8
C5 A:DO31002 3.5 14.0 0.8
C7 A:DO31002 3.5 14.2 0.8
C3 A:DO31002 3.5 13.6 0.8
C6 A:DO31002 3.5 14.7 0.8
C4 A:DO31002 3.5 13.7 0.8
C1 A:DO31002 3.5 12.7 0.8
C2 A:DO31002 3.6 12.8 0.8
HC51 A:DO31002 3.7 15.1 0.8
HC81 A:DO31002 3.8 15.2 0.8
HC32 A:DO31002 3.8 14.5 0.8
HC72 A:DO31002 3.8 15.4 0.8
HC12 A:DO31002 3.8 14.9 0.8
HC42 A:DO31002 3.8 14.7 0.8
HC61 A:DO31002 3.9 15.3 0.8
O A:HOH1360 3.9 31.8 0.6
HC22 A:DO31002 3.9 14.6 0.8
HA A:DO31002 4.1 15.3 0.8
H173 A:DO31002 4.1 15.7 0.8
H102 A:DO31002 4.1 15.7 0.8
H141 A:DO31002 4.1 14.6 0.8
O A:HOH1109 4.2 18.7 0.9
H121 A:DO31002 4.2 13.6 0.8
O6 A:DO31002 4.2 14.8 0.8
H162 A:DO31002 4.3 15.2 0.8
O A:HOH1118 4.3 10.0 0.7
C17 A:DO31002 4.3 16.2 0.8
HC82 A:DO31002 4.3 15.2 0.8
HC62 A:DO31002 4.3 15.3 0.8
HC71 A:DO31002 4.3 15.4 0.8
HC52 A:DO31002 4.4 15.1 0.8
HC41 A:DO31002 4.4 14.7 0.8
HC31 A:DO31002 4.4 14.5 0.8
O4 A:DO31002 4.4 13.5 0.8
HC11 A:DO31002 4.4 14.9 0.8
O2 A:DO31002 4.4 11.8 0.8
HC21 A:DO31002 4.4 14.6 0.8
O1 A:DO31004 4.4 10.1 0.7
O A:HOH1234 4.6 33.5 1.0
O A:HOH1110 4.6 35.0 1.0
O2 A:DO31004 4.7 14.7 0.7
H172 A:DO31002 4.8 15.7 0.8
O A:HOH1349 4.8 31.1 0.9
O A:HOH1278 4.9 30.2 0.8
C9 A:DO31004 4.9 11.1 0.7
O A:HOH1352 5.0 29.4 0.9

Gadolinium binding site 2 out of 4 in 8rt2

Go back to Gadolinium Binding Sites List in 8rt2
Gadolinium binding site 2 out of 4 in the Hen Egg White Lysozyme Crystallized with Bioassembler on Earth


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Hen Egg White Lysozyme Crystallized with Bioassembler on Earth within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1001

b:14.7
occ:0.24
GD A:GD1001 0.0 14.7 0.2
GD A:GD1001 1.3 10.0 0.8
O3 A:DO31002 1.5 10.7 0.8
O A:HOH1127 1.6 12.4 0.8
O5 A:DO31002 2.3 12.7 0.8
O1 A:DO31002 2.4 11.7 0.8
HO7 A:DO31002 2.4 14.4 0.8
C11 A:DO31002 2.5 12.3 0.8
C13 A:DO31002 2.8 14.2 0.8
O A:HOH1360 2.8 31.8 0.6
O A:HOH1109 2.9 18.7 0.9
O7 A:DO31002 3.0 12.5 0.8
N2 A:DO31002 3.1 11.4 0.8
C12 A:DO31002 3.2 12.2 0.8
H142 A:DO31002 3.2 14.6 0.8
N3 A:DO31002 3.2 13.0 0.8
C14 A:DO31002 3.3 13.7 0.8
H122 A:DO31002 3.4 13.6 0.8
O A:HOH1118 3.5 10.0 0.7
C9 A:DO31002 3.5 11.6 0.8
O4 A:DO31002 3.5 13.5 0.8
N1 A:DO31002 3.7 11.7 0.8
O A:HOH1278 3.7 30.2 0.8
O6 A:DO31002 3.7 14.8 0.8
HC32 A:DO31002 3.8 14.5 0.8
N4 A:DO31002 3.8 13.7 0.8
O A:HOH1110 3.8 35.0 1.0
C3 A:DO31002 3.9 13.6 0.8
O1 A:DO31004 3.9 10.1 0.7
C10 A:DO31002 4.0 12.7 0.8
H121 A:DO31002 4.1 13.6 0.8
H101 A:DO31002 4.1 15.7 0.8
C4 A:DO31002 4.1 13.7 0.8
C15 A:DO31002 4.1 14.6 0.8
O A:HOH1234 4.1 33.5 1.0
H161 A:DO31002 4.2 15.2 0.8
H141 A:DO31002 4.2 14.6 0.8
C2 A:DO31002 4.3 12.8 0.8
C5 A:DO31002 4.3 14.0 0.8
C16 A:DO31002 4.3 13.8 0.8
H173 A:DO31002 4.3 15.7 0.8
C1 A:DO31002 4.4 12.7 0.8
HC51 A:DO31002 4.4 15.1 0.8
HC12 A:DO31002 4.4 14.9 0.8
O A:HOH1112 4.6 30.9 0.8
O A:HOH1297 4.6 32.5 1.0
C6 A:DO31002 4.6 14.7 0.8
O3 A:DO31004 4.6 13.2 0.7
HC42 A:DO31002 4.6 14.7 0.8
O2 A:DO31002 4.6 11.8 0.8
C8 A:DO31002 4.7 13.5 0.8
C9 A:DO31004 4.7 11.1 0.7
C17 A:DO31002 4.8 16.2 0.8
HC22 A:DO31002 4.8 14.6 0.8
C7 A:DO31002 4.8 14.2 0.8
O2 A:DO31004 4.8 14.7 0.7
HC31 A:DO31002 4.8 14.5 0.8
HC41 A:DO31002 4.8 14.7 0.8
C11 A:DO31004 4.9 13.7 0.7
HA A:DO31002 4.9 15.3 0.8
HC21 A:DO31002 4.9 14.6 0.8
HC81 A:DO31002 5.0 15.2 0.8
H102 A:DO31002 5.0 15.7 0.8
HC72 A:DO31002 5.0 15.4 0.8

Gadolinium binding site 3 out of 4 in 8rt2

Go back to Gadolinium Binding Sites List in 8rt2
Gadolinium binding site 3 out of 4 in the Hen Egg White Lysozyme Crystallized with Bioassembler on Earth


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Hen Egg White Lysozyme Crystallized with Bioassembler on Earth within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1003

b:8.9
occ:0.73
GD A:GD1003 0.0 8.9 0.7
HO7 A:DO31004 1.6 12.4 0.7
O7 A:DO31004 2.3 10.6 0.7
O5 A:DO31004 2.3 9.8 0.7
O3 A:DO31004 2.4 13.2 0.7
O1 A:DO31004 2.4 10.1 0.7
O A:HOH1118 2.4 10.0 0.7
N1 A:DO31004 2.6 11.7 0.7
GD A:GD1003 2.6 11.3 0.3
N4 A:DO31004 2.6 10.7 0.7
N3 A:DO31004 2.6 11.9 0.7
N2 A:DO31004 2.7 12.9 0.7
C13 A:DO31004 3.1 10.6 0.7
C10 A:DO31004 3.2 12.9 0.7
H101 A:DO31004 3.2 13.9 0.7
C9 A:DO31004 3.2 11.1 0.7
C14 A:DO31004 3.2 12.6 0.7
C11 A:DO31004 3.3 13.7 0.7
H142 A:DO31004 3.3 14.6 0.7
C12 A:DO31004 3.3 12.6 0.7
C16 A:DO31004 3.4 10.6 0.7
C5 A:DO31004 3.4 13.3 0.7
H122 A:DO31004 3.5 15.4 0.7
C15 A:DO31004 3.5 10.5 0.7
C6 A:DO31004 3.5 12.3 0.7
H161 A:DO31004 3.5 13.8 0.7
C1 A:DO31004 3.5 14.1 0.7
C8 A:DO31004 3.5 13.2 0.7
C7 A:DO31004 3.5 13.0 0.7
C4 A:DO31004 3.6 13.1 0.7
C3 A:DO31004 3.6 14.2 0.7
C2 A:DO31004 3.6 14.0 0.7
HC52 A:DO31004 3.6 14.9 0.7
HC12 A:DO31004 3.7 14.9 0.7
HC82 A:DO31004 3.8 14.5 0.7
HC71 A:DO31004 3.8 14.4 0.7
HC61 A:DO31004 3.8 14.8 0.7
HC31 A:DO31004 3.9 15.4 0.7
HC42 A:DO31004 3.9 15.2 0.7
HC22 A:DO31004 3.9 15.2 0.7
O A:HOH1109 4.0 18.7 0.9
HA A:DO31004 4.1 13.7 0.7
H102 A:DO31004 4.1 13.9 0.7
H141 A:DO31004 4.1 14.6 0.7
O A:HOH1127 4.2 12.4 0.8
H121 A:DO31004 4.3 15.4 0.7
H173 A:DO31004 4.3 14.2 0.7
HC62 A:DO31004 4.3 14.8 0.7
HC51 A:DO31004 4.3 14.9 0.7
O1 A:DO31002 4.3 11.7 0.8
O6 A:DO31004 4.3 12.4 0.7
HC81 A:DO31004 4.4 14.5 0.7
HC72 A:DO31004 4.4 14.4 0.7
HC11 A:DO31004 4.4 14.9 0.7
O2 A:DO31004 4.4 14.7 0.7
HC41 A:DO31004 4.4 15.2 0.7
HC21 A:DO31004 4.4 15.2 0.7
HC32 A:DO31004 4.4 15.4 0.7
O4 A:DO31004 4.5 16.4 0.7
O A:HOH1360 4.5 31.8 0.6
C17 A:DO31004 4.5 11.9 0.7
O2 A:DO31002 4.5 11.8 0.8
O A:HOH1394 4.7 14.6 0.9
O A:HOH1293 4.8 32.9 1.0
C9 A:DO31002 4.8 11.6 0.8
O A:HOH1395 4.8 13.2 0.7
H172 A:DO31004 4.9 14.2 0.7

Gadolinium binding site 4 out of 4 in 8rt2

Go back to Gadolinium Binding Sites List in 8rt2
Gadolinium binding site 4 out of 4 in the Hen Egg White Lysozyme Crystallized with Bioassembler on Earth


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Hen Egg White Lysozyme Crystallized with Bioassembler on Earth within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1003

b:11.3
occ:0.27
GD A:GD1003 0.0 11.3 0.3
N2 A:DO31004 0.9 12.9 0.7
C2 A:DO31004 1.3 14.0 0.7
C12 A:DO31004 1.5 12.6 0.7
H122 A:DO31004 1.5 15.4 0.7
C1 A:DO31004 1.8 14.1 0.7
HC21 A:DO31004 1.9 15.2 0.7
HC12 A:DO31004 1.9 14.9 0.7
HC22 A:DO31004 2.1 15.2 0.7
H121 A:DO31004 2.2 15.4 0.7
C3 A:DO31004 2.3 14.2 0.7
N1 A:DO31004 2.3 11.7 0.7
C11 A:DO31004 2.6 13.7 0.7
GD A:GD1003 2.6 8.9 0.7
HC11 A:DO31004 2.7 14.9 0.7
HC32 A:DO31004 2.7 15.4 0.7
O1 A:DO31004 2.8 10.1 0.7
HC31 A:DO31004 2.8 15.4 0.7
O3 A:DO31004 2.9 13.2 0.7
C4 A:DO31004 3.2 13.1 0.7
C9 A:DO31004 3.3 11.1 0.7
HC82 A:DO31004 3.3 14.5 0.7
C10 A:DO31004 3.3 12.9 0.7
HC42 A:DO31004 3.4 15.2 0.7
C8 A:DO31004 3.4 13.2 0.7
N3 A:DO31004 3.5 11.9 0.7
O4 A:DO31004 3.7 16.4 0.7
HO7 A:DO31004 3.8 12.4 0.7
O A:HOH1337 3.9 34.2 0.9
H102 A:DO31004 3.9 13.9 0.7
H142 A:DO31004 4.0 14.6 0.7
H101 A:DO31004 4.0 13.9 0.7
HC81 A:DO31004 4.1 14.5 0.7
HC41 A:DO31004 4.1 15.2 0.7
O A:HOH1234 4.1 33.5 1.0
N4 A:DO31004 4.2 10.7 0.7
O A:HOH1360 4.2 31.8 0.6
O2 A:DO31004 4.3 14.7 0.7
C14 A:DO31004 4.3 12.6 0.7
HC61 A:DO31004 4.3 14.8 0.7
C7 A:DO31004 4.4 13.0 0.7
O A:HOH1118 4.5 10.0 0.7
O7 A:DO31004 4.5 10.6 0.7
C6 A:DO31004 4.6 12.3 0.7
C5 A:DO31004 4.6 13.3 0.7
O A:HOH1127 4.6 12.4 0.8
O5 A:DO31004 4.7 9.8 0.7
HC71 A:DO31004 4.9 14.4 0.7
O A:HOH1109 5.0 18.7 0.9

Reference:

C.Maccarthy, E.V.Koudan, S.V.Petrov, A.A.Levin, Y.D.Khesuani, V.Borshchevskiy. Hen Egg White Lysozyme Crystallized with Bioassembler on Earth To Be Published.
Page generated: Sat Aug 10 22:50:59 2024

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